commit 491b9a4d696258fdba883684caa26a08c1b036f1
Author: HSE Student <golovin@fbb.msu.ru>
Date:   Fri Nov 3 15:30:02 2017 -0300

    md test

diff --git a/example/modeller_cox3.md b/example/modeller_cox3.md
new file mode 100644
index 0000000..7d2227b
--- /dev/null
+++ b/example/modeller_cox3.md
@@ -0,0 +1,4560 @@
+
+
+```python
+import sys 
+sys.path.append('/usr/lib/modeller9.12/modlib/')
+sys.path.append('/usr/lib/modeller9.12/lib/x86_64-intel8/python2.5/')
+import modeller 
+import _modeller
+import modeller.automodel 
+#impo modeller.automodel import *
+```
+
+
+```python
+env=modeller.environ()
+env.io.hetatm=False #True
+
+```
+
+
+```python
+cd /home/domain/anur/work/cox3
+```
+
+    /home/domain/anur/work/cox3
+
+
+
+```python
+alignm=modeller.alignment(env)
+alignm.append(file='COX3.fasta', align_codes='all',alignment_format='FASTA')
+mdl1 = modeller.model(env, file='1v55.pdb', model_segment=('FIRST:'+'C', 'LAST:'+'C'))
+mdl2 = modeller.model(env, file='1v55.pdb', model_segment=('FIRST:'+'P', 'LAST:'+'P'))
+alignm.append_model(mdl1, atom_files='1v55.pdb', align_codes='1v55_C')
+alignm.append_model(mdl2, atom_files='1v55.pdb', align_codes='1v55_P')
+
+```
+
+
+```python
+alignm.salign()
+s= alignm[0]
+for i in range(len(alignm)):
+    print "%s identical to wt in %4.1f perc" %(alignm[i].code,s.get_sequence_identity(alignm[i]))
+aln.write(file='all_in_one.ali', alignment_format='PIR')
+```
+
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    2
+    
+    SALIGN_____> adding the next group to the alignment; iteration    3
+    
+    SALIGN_____> adding the next group to the alignment; iteration    4
+    
+    SALIGN_____> adding the next group to the alignment; iteration    5
+    
+    SALIGN_____> adding the next group to the alignment; iteration    6
+    
+    SALIGN_____> adding the next group to the alignment; iteration    7
+    
+    SALIGN_____> adding the next group to the alignment; iteration    8
+    
+    SALIGN_____> adding the next group to the alignment; iteration    9
+    
+    SALIGN_____> adding the next group to the alignment; iteration   10
+    
+    SALIGN_____> adding the next group to the alignment; iteration   11
+    9913 identical to wt in 100.0 perc
+    9606_V identical to wt in 87.7 perc
+    9606_A identical to wt in 87.4 perc
+    9606_I identical to wt in 87.4 perc
+    9606_F identical to wt in 87.4 perc
+    9606_S identical to wt in 87.4 perc
+    9606_L identical to wt in 87.4 perc
+    9606_M identical to wt in 87.4 perc
+    9606_E identical to wt in 87.4 perc
+    9606_T identical to wt in 87.4 perc
+    1v55_C identical to wt in 100.0 perc
+    1v55_P identical to wt in 100.0 perc
+
+
+
+```python
+for s in aln[:-2]:
+    print s.code
+    a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns= ('1v55_C','1v55_P'), sequence = s.code )
+    a.name='mod'+s.code
+    a.starting_model = 1
+    a.ending_model = 1
+    a.make()
+    
+```
+
+    9913
+    automodel__W> Topology and/or parameter libraries already in memory. These will
+                    be used instead of the automodel defaults. If this is not what you
+                    want, clear them before creating the automodel object with
+                    env.libs.topology.clear() and env.libs.parameters.clear()
+    
+    
+    check_ali___> Checking pairwise structural superpositions. 
+    
+    Equivalent CA pairs with distance difference larger than  6.0 angstroms:
+    
+    ALN_POS TMPL1 TMPL2  RID1  RID2  NAM1  NAM2     DIST
+    ----------------------------------------------------
+    END OF TABLE
+    
+    check_ali___> Checking the sequence-structure alignment. 
+    
+    Implied target CA(i)-CA(i+1) distances longer than  8.0 angstroms:
+    
+    ALN_POS  TMPL  RID1  RID2  NAM1  NAM2     DIST
+    ----------------------------------------------
+    END OF TABLE
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16   261
+                  atom names           : C     +N
+                  atom indices         :  2123     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16   261
+                  atom names           : C     CA    +N    O
+                  atom indices         :  2123  2120     0  2124
+    mdtrsr__446W> A potential that relies on one protein is used, yet you have at
+                  least one known structure available. MDT, not library, potential is used.
+    0 atoms in HETATM/BLK residues constrained
+    to protein atoms within 2.30 angstroms
+    and protein CA atoms within 10.00 angstroms
+    0 atoms in residues without defined topology
+    constrained to be rigid bodies
+    condens_443_> Restraints marked for deletion were removed.
+                  Total number of restraints before, now:    26595    24757
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    
+    
+    >> ENERGY; Differences between the model's features and restraints:
+    Number of all residues in MODEL                   :      261
+    Number of all, selected real atoms                :     2125    2125
+    Number of all, selected pseudo atoms              :        0       0
+    Number of all static, selected restraints         :    24757   24757
+    COVALENT_CYS                                      :        F
+    NONBONDED_SEL_ATOMS                               :        1
+    Number of non-bonded pairs (excluding 1-2,1-3,1-4):     4695
+    Dynamic pairs routine                             : 2, NATM x NATM cell sorting
+    Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
+    LENNARD_JONES_SWITCH                              :    6.500   7.500
+    COULOMB_JONES_SWITCH                              :    6.500   7.500
+    RESIDUE_SPAN_RANGE                                :        0   99999
+    NLOGN_USE                                         :       15
+    CONTACT_SHELL                                     :    4.000
+    DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
+    SPHERE_STDV                                       :    0.050
+    RADII_FACTOR                                      :    0.820
+    Current energy                                    :        7158.1758
+    
+    
+    
+    
+    
+    Summary of the restraint violations: 
+    
+       NUM     ... number of restraints.
+       NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
+       RVIOL   ... relative difference from the best value.
+       NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
+       RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
+       RMS_2   ... RMS(feature, best_value, NUMB).
+       MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
+    
+     #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
+    ------------------------------------------------------------------------------------------------------
+     1 Bond length potential              :    2212       0      0   0.004   0.004      11.948       1.000
+     2 Bond angle potential               :    3027       0      2   1.873   1.873      208.11       1.000
+     3 Stereochemical cosine torsion poten:    1709       0     19  38.273  38.273      369.73       1.000
+     4 Stereochemical improper torsion pot:    1048       0      1   1.125   1.125      25.935       1.000
+     5 Soft-sphere overlap restraints     :    4695       0      0   0.001   0.001     0.43761       1.000
+     6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
+     7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
+     8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
+     9 Distance restraints 1 (CA-CA)      :    4433       0      2   0.120   0.120      586.51       1.000
+    10 Distance restraints 2 (N-O)        :    4608       0      0   0.133   0.133      869.96       1.000
+    11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
+    12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
+    13 Mainchain Omega dihedral restraints:     260       0      2   3.409   3.409      34.801       1.000
+    14 Sidechain Chi_1 dihedral restraints:     226       0      1  46.061  46.061      13.243       1.000
+    15 Sidechain Chi_2 dihedral restraints:     165       0      2  63.301  63.301      33.559       1.000
+    16 Sidechain Chi_3 dihedral restraints:      46       0      0  69.837  69.837      26.999       1.000
+    17 Sidechain Chi_4 dihedral restraints:       8       0      0 125.128 125.128      7.1805       1.000
+    18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
+    19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
+    20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
+    21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    23 Distance restraints 3 (SDCH-MNCH)  :    4161       0      0   0.334   0.334      2942.5       1.000
+    24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
+    25 Phi/Psi pair of dihedral restraints:     259       3      9  15.024  19.220     -172.15       1.000
+    26 Distance restraints 4 (SDCH-SDCH)  :    2595       0     12   0.772   0.772      2199.4       1.000
+    27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
+    28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
+    29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
+    30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
+    31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
+    32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
+    34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
+    35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
+    36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
+    37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
+    38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
+    39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000
+    
+    
+    
+    # Heavy relative violation of each residue is written to: 9913.V99990001
+    # The profile is NOT normalized by the number of restraints.
+    # The profiles are smoothed over a window of residues:    1
+    # The sum of all numbers in the file:   18744.2441
+    
+    
+    
+    List of the violated restraints:
+       A restraint is violated when the relative difference
+       from the best value (RVIOL) is larger than CUTOFF.
+    
+       ICSR   ... index of a restraint in the current set.
+       RESNO  ... residue numbers of the first two atoms.
+       ATM    ... IUPAC atom names of the first two atoms.
+       FEAT   ... the value of the feature in the model.
+       restr  ... the mean of the basis restraint with the smallest
+                  difference from the model (local minimum).
+       viol   ... difference from the local minimum.
+       rviol  ... relative difference from the local minimum.
+       RESTR  ... the best value (global minimum).
+       VIOL   ... difference from the best value.
+       RVIOL  ... relative difference from the best value.
+    
+    
+    -------------------------------------------------------------------------------------------------
+    
+    Feature 25                           : Phi/Psi pair of dihedral restraints     
+    List of the RVIOL violations larger than   :       6.5000
+    
+        #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
+        1   7997   1M   2T C   N       7    9  -90.07  -78.10   21.48    0.71  -63.20  152.65   21.37
+        1          2T   2T N   CA      9   10  167.63  149.80                  -42.10
+        2   8123 127L 128E C   N    1023 1025  -85.08  -63.60   83.66   12.37  -69.30   97.63    6.89
+        2        128E 128E N   CA   1025 1026 -121.16  -40.30                  142.50
+        3   8227 231H 232H C   N    1849 1851 -111.37  -63.20   75.39    8.23  -63.20   75.39    8.23
+        3        232H 232H N   CA   1851 1852   15.69  -42.30                  -42.30
+    
+    
+    report______> Distribution of short non-bonded contacts:
+    
+    
+    DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
+    DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
+    FREQUENCY:     0    0    0    0    0    7   11   61  168  215  199  279  378  411  383
+    
+    
+    << end of ENERGY.
+    
+    >> Summary of successfully produced models:
+    Filename                          molpdf
+    ----------------------------------------
+    9913.B99990001.pdb            7158.17578
+    
+    9606_V
+    automodel__W> Topology and/or parameter libraries already in memory. These will
+                    be used instead of the automodel defaults. If this is not what you
+                    want, clear them before creating the automodel object with
+                    env.libs.topology.clear() and env.libs.parameters.clear()
+    
+    
+    check_ali___> Checking pairwise structural superpositions. 
+    
+    Equivalent CA pairs with distance difference larger than  6.0 angstroms:
+    
+    ALN_POS TMPL1 TMPL2  RID1  RID2  NAM1  NAM2     DIST
+    ----------------------------------------------------
+    END OF TABLE
+    
+    check_ali___> Checking the sequence-structure alignment. 
+    
+    Implied target CA(i)-CA(i+1) distances longer than  8.0 angstroms:
+    
+    ALN_POS  TMPL  RID1  RID2  NAM1  NAM2     DIST
+    ----------------------------------------------
+    END OF TABLE
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16   261
+                  atom names           : C     +N
+                  atom indices         :  2125     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16   261
+                  atom names           : C     CA    +N    O
+                  atom indices         :  2125  2122     0  2126
+    mdtrsr__446W> A potential that relies on one protein is used, yet you have at
+                  least one known structure available. MDT, not library, potential is used.
+    0 atoms in HETATM/BLK residues constrained
+    to protein atoms within 2.30 angstroms
+    and protein CA atoms within 10.00 angstroms
+    0 atoms in residues without defined topology
+    constrained to be rigid bodies
+    condens_443_> Restraints marked for deletion were removed.
+                  Total number of restraints before, now:    26187    24337
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    
+    
+    >> ENERGY; Differences between the model's features and restraints:
+    Number of all residues in MODEL                   :      261
+    Number of all, selected real atoms                :     2127    2127
+    Number of all, selected pseudo atoms              :        0       0
+    Number of all static, selected restraints         :    24337   24337
+    COVALENT_CYS                                      :        F
+    NONBONDED_SEL_ATOMS                               :        1
+    Number of non-bonded pairs (excluding 1-2,1-3,1-4):     4811
+    Dynamic pairs routine                             : 2, NATM x NATM cell sorting
+    Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
+    LENNARD_JONES_SWITCH                              :    6.500   7.500
+    COULOMB_JONES_SWITCH                              :    6.500   7.500
+    RESIDUE_SPAN_RANGE                                :        0   99999
+    NLOGN_USE                                         :       15
+    CONTACT_SHELL                                     :    4.000
+    DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
+    SPHERE_STDV                                       :    0.050
+    RADII_FACTOR                                      :    0.820
+    Current energy                                    :        6565.6021
+    
+    
+    
+    
+    
+    Summary of the restraint violations: 
+    
+       NUM     ... number of restraints.
+       NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
+       RVIOL   ... relative difference from the best value.
+       NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
+       RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
+       RMS_2   ... RMS(feature, best_value, NUMB).
+       MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
+    
+     #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
+    ------------------------------------------------------------------------------------------------------
+     1 Bond length potential              :    2214       0      0   0.004   0.004      10.728       1.000
+     2 Bond angle potential               :    3030       0      2   1.780   1.780      190.34       1.000
+     3 Stereochemical cosine torsion poten:    1707       0     16  38.781  38.781      372.96       1.000
+     4 Stereochemical improper torsion pot:    1045       0      0   1.058   1.058      23.385       1.000
+     5 Soft-sphere overlap restraints     :    4811       0      0   0.001   0.001      1.0434       1.000
+     6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
+     7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
+     8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
+     9 Distance restraints 1 (CA-CA)      :    4433       0      0   0.094   0.094      588.07       1.000
+    10 Distance restraints 2 (N-O)        :    4608       0      0   0.117   0.117      689.60       1.000
+    11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
+    12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
+    13 Mainchain Omega dihedral restraints:     260       0      1   3.209   3.209      30.726       1.000
+    14 Sidechain Chi_1 dihedral restraints:     227       0      1  54.523  54.523      23.232       1.000
+    15 Sidechain Chi_2 dihedral restraints:     168       0      1  61.214  61.214      40.466       1.000
+    16 Sidechain Chi_3 dihedral restraints:      48       0      0  58.055  58.055      24.592       1.000
+    17 Sidechain Chi_4 dihedral restraints:       8       0      0 120.815 120.815      4.9296       1.000
+    18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
+    19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
+    20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
+    21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    23 Distance restraints 3 (SDCH-MNCH)  :    3900       0      0   0.332   0.332      2735.1       1.000
+    24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
+    25 Phi/Psi pair of dihedral restraints:     259       3     10  14.794  19.369     -174.12       1.000
+    26 Distance restraints 4 (SDCH-SDCH)  :    2430       0     11   0.714   0.714      2004.5       1.000
+    27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
+    28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
+    29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
+    30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
+    31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
+    32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
+    34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
+    35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
+    36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
+    37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
+    38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
+    39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000
+    
+    
+    
+    # Heavy relative violation of each residue is written to: 9606_V.V99990001
+    # The profile is NOT normalized by the number of restraints.
+    # The profiles are smoothed over a window of residues:    1
+    # The sum of all numbers in the file:   18410.9668
+    
+    
+    
+    List of the violated restraints:
+       A restraint is violated when the relative difference
+       from the best value (RVIOL) is larger than CUTOFF.
+    
+       ICSR   ... index of a restraint in the current set.
+       RESNO  ... residue numbers of the first two atoms.
+       ATM    ... IUPAC atom names of the first two atoms.
+       FEAT   ... the value of the feature in the model.
+       restr  ... the mean of the basis restraint with the smallest
+                  difference from the model (local minimum).
+       viol   ... difference from the local minimum.
+       rviol  ... relative difference from the local minimum.
+       RESTR  ... the best value (global minimum).
+       VIOL   ... difference from the best value.
+       RVIOL  ... relative difference from the best value.
+    
+    
+    -------------------------------------------------------------------------------------------------
+    
+    Feature 25                           : Phi/Psi pair of dihedral restraints     
+    List of the RVIOL violations larger than   :       6.5000
+    
+        #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
+        1   7997   1M   2T C   N       7    9  -73.89  -78.10    5.52    0.36  -63.20  164.87   21.85
+        1          2T   2T N   CA      9   10  153.38  149.80                  -42.10
+        2   8123 127L 128E C   N    1026 1028  -86.32  -63.60   82.64   12.30  -69.30   99.21    6.96
+        2        128E 128E N   CA   1028 1029 -119.76  -40.30                  142.50
+        3   8227 231H 232H C   N    1851 1853 -113.42  -63.20   79.87    8.68  -63.20   79.87    8.68
+        3        232H 232H N   CA   1853 1854   19.80  -42.30                  -42.30
+    
+    
+    report______> Distribution of short non-bonded contacts:
+    
+    
+    DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
+    DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
+    FREQUENCY:     0    0    0    0    0    9   17   72  217  228  179  284  367  429  353
+    
+    
+    << end of ENERGY.
+    
+    >> Summary of successfully produced models:
+    Filename                          molpdf
+    ----------------------------------------
+    9606_V.B99990001.pdb          6565.60205
+    
+    9606_A
+    automodel__W> Topology and/or parameter libraries already in memory. These will
+                    be used instead of the automodel defaults. If this is not what you
+                    want, clear them before creating the automodel object with
+                    env.libs.topology.clear() and env.libs.parameters.clear()
+    
+    
+    check_ali___> Checking pairwise structural superpositions. 
+    
+    Equivalent CA pairs with distance difference larger than  6.0 angstroms:
+    
+    ALN_POS TMPL1 TMPL2  RID1  RID2  NAM1  NAM2     DIST
+    ----------------------------------------------------
+    END OF TABLE
+    
+    check_ali___> Checking the sequence-structure alignment. 
+    
+    Implied target CA(i)-CA(i+1) distances longer than  8.0 angstroms:
+    
+    ALN_POS  TMPL  RID1  RID2  NAM1  NAM2     DIST
+    ----------------------------------------------
+    END OF TABLE
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16   261
+                  atom names           : C     +N
+                  atom indices         :  2123     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16   261
+                  atom names           : C     CA    +N    O
+                  atom indices         :  2123  2120     0  2124
+    mdtrsr__446W> A potential that relies on one protein is used, yet you have at
+                  least one known structure available. MDT, not library, potential is used.
+    0 atoms in HETATM/BLK residues constrained
+    to protein atoms within 2.30 angstroms
+    and protein CA atoms within 10.00 angstroms
+    0 atoms in residues without defined topology
+    constrained to be rigid bodies
+    condens_443_> Restraints marked for deletion were removed.
+                  Total number of restraints before, now:    26163    24314
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_484W> Dihedral still outside +-90:       90.0977
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    
+    
+    >> ENERGY; Differences between the model's features and restraints:
+    Number of all residues in MODEL                   :      261
+    Number of all, selected real atoms                :     2125    2125
+    Number of all, selected pseudo atoms              :        0       0
+    Number of all static, selected restraints         :    24314   24314
+    COVALENT_CYS                                      :        F
+    NONBONDED_SEL_ATOMS                               :        1
+    Number of non-bonded pairs (excluding 1-2,1-3,1-4):     4761
+    Dynamic pairs routine                             : 2, NATM x NATM cell sorting
+    Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
+    LENNARD_JONES_SWITCH                              :    6.500   7.500
+    COULOMB_JONES_SWITCH                              :    6.500   7.500
+    RESIDUE_SPAN_RANGE                                :        0   99999
+    NLOGN_USE                                         :       15
+    CONTACT_SHELL                                     :    4.000
+    DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
+    SPHERE_STDV                                       :    0.050
+    RADII_FACTOR                                      :    0.820
+    Current energy                                    :        6569.2383
+    
+    
+    
+    
+    
+    Summary of the restraint violations: 
+    
+       NUM     ... number of restraints.
+       NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
+       RVIOL   ... relative difference from the best value.
+       NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
+       RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
+       RMS_2   ... RMS(feature, best_value, NUMB).
+       MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
+    
+     #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
+    ------------------------------------------------------------------------------------------------------
+     1 Bond length potential              :    2212       0      0   0.004   0.004      11.764       1.000
+     2 Bond angle potential               :    3027       0      3   1.803   1.803      193.50       1.000
+     3 Stereochemical cosine torsion poten:    1704       0     17  38.650  38.650      371.69       1.000
+     4 Stereochemical improper torsion pot:    1044       0      0   1.071   1.071      24.081       1.000
+     5 Soft-sphere overlap restraints     :    4761       0      0   0.001   0.001     0.95893       1.000
+     6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
+     7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
+     8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
+     9 Distance restraints 1 (CA-CA)      :    4433       0      0   0.094   0.094      588.59       1.000
+    10 Distance restraints 2 (N-O)        :    4608       0      0   0.118   0.118      687.22       1.000
+    11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
+    12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
+    13 Mainchain Omega dihedral restraints:     260       0      1   3.305   3.305      32.628       1.000
+    14 Sidechain Chi_1 dihedral restraints:     226       0      0  51.035  51.035      11.649       1.000
+    15 Sidechain Chi_2 dihedral restraints:     168       0      1  60.161  60.161      31.284       1.000
+    16 Sidechain Chi_3 dihedral restraints:      48       0      0  48.215  48.215      25.921       1.000
+    17 Sidechain Chi_4 dihedral restraints:       8       0      0  71.145  71.145      6.3579       1.000
+    18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
+    19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
+    20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
+    21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    23 Distance restraints 3 (SDCH-MNCH)  :    3891       0      0   0.350   0.350      2733.9       1.000
+    24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
+    25 Phi/Psi pair of dihedral restraints:     259       3      8  14.878  19.641     -174.12       1.000
+    26 Distance restraints 4 (SDCH-SDCH)  :    2426       0      7   0.754   0.754      2023.8       1.000
+    27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
+    28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
+    29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
+    30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
+    31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
+    32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
+    34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
+    35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
+    36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
+    37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
+    38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
+    39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000
+    
+    
+    
+    # Heavy relative violation of each residue is written to: 9606_A.V99990001
+    # The profile is NOT normalized by the number of restraints.
+    # The profiles are smoothed over a window of residues:    1
+    # The sum of all numbers in the file:   17983.2812
+    
+    
+    
+    List of the violated restraints:
+       A restraint is violated when the relative difference
+       from the best value (RVIOL) is larger than CUTOFF.
+    
+       ICSR   ... index of a restraint in the current set.
+       RESNO  ... residue numbers of the first two atoms.
+       ATM    ... IUPAC atom names of the first two atoms.
+       FEAT   ... the value of the feature in the model.
+       restr  ... the mean of the basis restraint with the smallest
+                  difference from the model (local minimum).
+       viol   ... difference from the local minimum.
+       rviol  ... relative difference from the local minimum.
+       RESTR  ... the best value (global minimum).
+       VIOL   ... difference from the best value.
+       RVIOL  ... relative difference from the best value.
+    
+    
+    -------------------------------------------------------------------------------------------------
+    
+    Feature 25                           : Phi/Psi pair of dihedral restraints     
+    List of the RVIOL violations larger than   :       6.5000
+    
+        #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
+        1   7988   1M   2T C   N       7    9 -133.19 -124.80   17.39    0.55  -63.20  173.88   26.89
+        1          2T   2T N   CA      9   10  158.73  143.50                  -42.10
+        2   8114 127L 128E C   N    1024 1026  -86.72  -63.60   84.50   12.57  -69.30   97.50    6.82
+        2        128E 128E N   CA   1026 1027 -121.57  -40.30                  142.50
+        3   8218 231H 232H C   N    1849 1851 -114.73  -63.20   81.73    8.89  -63.20   81.73    8.89
+        3        232H 232H N   CA   1851 1852   21.13  -42.30                  -42.30
+    
+    
+    report______> Distribution of short non-bonded contacts:
+    
+    
+    DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
+    DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
+    FREQUENCY:     0    0    0    0    0    8   13   55  183  249  221  279  367  400  354
+    
+    
+    << end of ENERGY.
+    
+    >> Summary of successfully produced models:
+    Filename                          molpdf
+    ----------------------------------------
+    9606_A.B99990001.pdb          6569.23828
+    
+    9606_I
+    automodel__W> Topology and/or parameter libraries already in memory. These will
+                    be used instead of the automodel defaults. If this is not what you
+                    want, clear them before creating the automodel object with
+                    env.libs.topology.clear() and env.libs.parameters.clear()
+    
+    
+    check_ali___> Checking pairwise structural superpositions. 
+    
+    Equivalent CA pairs with distance difference larger than  6.0 angstroms:
+    
+    ALN_POS TMPL1 TMPL2  RID1  RID2  NAM1  NAM2     DIST
+    ----------------------------------------------------
+    END OF TABLE
+    
+    check_ali___> Checking the sequence-structure alignment. 
+    
+    Implied target CA(i)-CA(i+1) distances longer than  8.0 angstroms:
+    
+    ALN_POS  TMPL  RID1  RID2  NAM1  NAM2     DIST
+    ----------------------------------------------
+    END OF TABLE
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16   261
+                  atom names           : C     +N
+                  atom indices         :  2126     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16   261
+                  atom names           : C     CA    +N    O
+                  atom indices         :  2126  2123     0  2127
+    mdtrsr__446W> A potential that relies on one protein is used, yet you have at
+                  least one known structure available. MDT, not library, potential is used.
+    0 atoms in HETATM/BLK residues constrained
+    to protein atoms within 2.30 angstroms
+    and protein CA atoms within 10.00 angstroms
+    0 atoms in residues without defined topology
+    constrained to be rigid bodies
+    condens_443_> Restraints marked for deletion were removed.
+                  Total number of restraints before, now:    26179    24328
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    
+    
+    >> ENERGY; Differences between the model's features and restraints:
+    Number of all residues in MODEL                   :      261
+    Number of all, selected real atoms                :     2128    2128
+    Number of all, selected pseudo atoms              :        0       0
+    Number of all static, selected restraints         :    24328   24328
+    COVALENT_CYS                                      :        F
+    NONBONDED_SEL_ATOMS                               :        1
+    Number of non-bonded pairs (excluding 1-2,1-3,1-4):     4871
+    Dynamic pairs routine                             : 2, NATM x NATM cell sorting
+    Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
+    LENNARD_JONES_SWITCH                              :    6.500   7.500
+    COULOMB_JONES_SWITCH                              :    6.500   7.500
+    RESIDUE_SPAN_RANGE                                :        0   99999
+    NLOGN_USE                                         :       15
+    CONTACT_SHELL                                     :    4.000
+    DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
+    SPHERE_STDV                                       :    0.050
+    RADII_FACTOR                                      :    0.820
+    Current energy                                    :        6929.7739
+    
+    
+    
+    
+    
+    Summary of the restraint violations: 
+    
+       NUM     ... number of restraints.
+       NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
+       RVIOL   ... relative difference from the best value.
+       NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
+       RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
+       RMS_2   ... RMS(feature, best_value, NUMB).
+       MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
+    
+     #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
+    ------------------------------------------------------------------------------------------------------
+     1 Bond length potential              :    2215       0      1   0.006   0.006      18.748       1.000
+     2 Bond angle potential               :    3031       7      9   3.444   3.444      511.68       1.000
+     3 Stereochemical cosine torsion poten:    1708       0     16  38.513  38.513      368.84       1.000
+     4 Stereochemical improper torsion pot:    1045       0      0   1.028   1.028      21.971       1.000
+     5 Soft-sphere overlap restraints     :    4871       1      1   0.004   0.004      11.126       1.000
+     6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
+     7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
+     8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
+     9 Distance restraints 1 (CA-CA)      :    4433       0      0   0.095   0.095      588.96       1.000
+    10 Distance restraints 2 (N-O)        :    4608       0      0   0.119   0.119      684.27       1.000
+    11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
+    12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
+    13 Mainchain Omega dihedral restraints:     260       0      1   3.259   3.259      31.709       1.000
+    14 Sidechain Chi_1 dihedral restraints:     227       0      0  53.884  53.884      19.977       1.000
+    15 Sidechain Chi_2 dihedral restraints:     169       0      2  65.492  65.492      43.653       1.000
+    16 Sidechain Chi_3 dihedral restraints:      48       0      0  64.926  64.926      28.202       1.000
+    17 Sidechain Chi_4 dihedral restraints:       8       0      0  80.914  80.914      5.9267       1.000
+    18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
+    19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
+    20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
+    21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    23 Distance restraints 3 (SDCH-MNCH)  :    3891       0      0   0.340   0.340      2729.0       1.000
+    24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
+    25 Phi/Psi pair of dihedral restraints:     259       3      9  15.002  18.434     -174.51       1.000
+    26 Distance restraints 4 (SDCH-SDCH)  :    2426       0     14   0.785   0.785      2040.2       1.000
+    27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
+    28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
+    29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
+    30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
+    31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
+    32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
+    34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
+    35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
+    36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
+    37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
+    38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
+    39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000
+    
+    
+    
+    # Heavy relative violation of each residue is written to: 9606_I.V99990001
+    # The profile is NOT normalized by the number of restraints.
+    # The profiles are smoothed over a window of residues:    1
+    # The sum of all numbers in the file:   18748.8809
+    
+    
+    
+    List of the violated restraints:
+       A restraint is violated when the relative difference
+       from the best value (RVIOL) is larger than CUTOFF.
+    
+       ICSR   ... index of a restraint in the current set.
+       RESNO  ... residue numbers of the first two atoms.
+       ATM    ... IUPAC atom names of the first two atoms.
+       FEAT   ... the value of the feature in the model.
+       restr  ... the mean of the basis restraint with the smallest
+                  difference from the model (local minimum).
+       viol   ... difference from the local minimum.
+       rviol  ... relative difference from the local minimum.
+       RESTR  ... the best value (global minimum).
+       VIOL   ... difference from the best value.
+       RVIOL  ... relative difference from the best value.
+    
+    
+    -------------------------------------------------------------------------------------------------
+    
+    Feature  2                           : Bond angle potential                    
+    List of the RVIOL violations larger than   :       4.5000
+    
+        #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
+        1   5103 251F 251F CB  CG   2028 2029  152.26  122.30   29.96    6.51  122.30   29.96    6.51
+    
+    -------------------------------------------------------------------------------------------------
+    
+    Feature 25                           : Phi/Psi pair of dihedral restraints     
+    List of the RVIOL violations larger than   :       6.5000
+    
+        #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
+        1   8000   1M   2T C   N       7    9  -78.13  -78.10   12.53    0.53  -63.20  156.29   21.03
+        1          2T   2T N   CA      9   10  162.32  149.80                  -42.10
+        2   8126 127L 128E C   N    1027 1029  -80.62  -63.60   87.36   12.61  -69.30   92.21    6.63
+        2        128E 128E N   CA   1029 1030 -125.99  -40.30                  142.50
+        3   8230 231H 232H C   N    1852 1854 -114.01  -63.20   79.74    8.70  -63.20   79.74    8.70
+        3        232H 232H N   CA   1854 1855   19.15  -42.30                  -42.30
+    
+    
+    report______> Distribution of short non-bonded contacts:
+    
+    
+    DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
+    DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
+    FREQUENCY:     0    0    0    0    0   10   16   74  185  265  204  297  367  415  381
+    
+    
+    << end of ENERGY.
+    
+    >> Summary of successfully produced models:
+    Filename                          molpdf
+    ----------------------------------------
+    9606_I.B99990001.pdb          6929.77393
+    
+    9606_F
+    automodel__W> Topology and/or parameter libraries already in memory. These will
+                    be used instead of the automodel defaults. If this is not what you
+                    want, clear them before creating the automodel object with
+                    env.libs.topology.clear() and env.libs.parameters.clear()
+    
+    
+    check_ali___> Checking pairwise structural superpositions. 
+    
+    Equivalent CA pairs with distance difference larger than  6.0 angstroms:
+    
+    ALN_POS TMPL1 TMPL2  RID1  RID2  NAM1  NAM2     DIST
+    ----------------------------------------------------
+    END OF TABLE
+    
+    check_ali___> Checking the sequence-structure alignment. 
+    
+    Implied target CA(i)-CA(i+1) distances longer than  8.0 angstroms:
+    
+    ALN_POS  TMPL  RID1  RID2  NAM1  NAM2     DIST
+    ----------------------------------------------
+    END OF TABLE
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16   261
+                  atom names           : C     +N
+                  atom indices         :  2129     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16   261
+                  atom names           : C     CA    +N    O
+                  atom indices         :  2129  2126     0  2130
+    mdtrsr__446W> A potential that relies on one protein is used, yet you have at
+                  least one known structure available. MDT, not library, potential is used.
+    0 atoms in HETATM/BLK residues constrained
+    to protein atoms within 2.30 angstroms
+    and protein CA atoms within 10.00 angstroms
+    0 atoms in residues without defined topology
+    constrained to be rigid bodies
+    condens_443_> Restraints marked for deletion were removed.
+                  Total number of restraints before, now:    26199    24348
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    
+    
+    >> ENERGY; Differences between the model's features and restraints:
+    Number of all residues in MODEL                   :      261
+    Number of all, selected real atoms                :     2131    2131
+    Number of all, selected pseudo atoms              :        0       0
+    Number of all static, selected restraints         :    24348   24348
+    COVALENT_CYS                                      :        F
+    NONBONDED_SEL_ATOMS                               :        1
+    Number of non-bonded pairs (excluding 1-2,1-3,1-4):     4778
+    Dynamic pairs routine                             : 2, NATM x NATM cell sorting
+    Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
+    LENNARD_JONES_SWITCH                              :    6.500   7.500
+    COULOMB_JONES_SWITCH                              :    6.500   7.500
+    RESIDUE_SPAN_RANGE                                :        0   99999
+    NLOGN_USE                                         :       15
+    CONTACT_SHELL                                     :    4.000
+    DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
+    SPHERE_STDV                                       :    0.050
+    RADII_FACTOR                                      :    0.820
+    Current energy                                    :        6458.9883
+    
+    
+    
+    
+    
+    Summary of the restraint violations: 
+    
+       NUM     ... number of restraints.
+       NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
+       RVIOL   ... relative difference from the best value.
+       NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
+       RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
+       RMS_2   ... RMS(feature, best_value, NUMB).
+       MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
+    
+     #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
+    ------------------------------------------------------------------------------------------------------
+     1 Bond length potential              :    2219       0      0   0.004   0.004      10.494       1.000
+     2 Bond angle potential               :    3036       0      2   1.731   1.731      180.53       1.000
+     3 Stereochemical cosine torsion poten:    1714       0     15  38.612  38.612      367.11       1.000
+     4 Stereochemical improper torsion pot:    1050       0      0   0.952   0.952      19.641       1.000
+     5 Soft-sphere overlap restraints     :    4778       0      0   0.001   0.001     0.58739       1.000
+     6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
+     7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
+     8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
+     9 Distance restraints 1 (CA-CA)      :    4433       0      0   0.088   0.088      582.88       1.000
+    10 Distance restraints 2 (N-O)        :    4608       0      0   0.116   0.116      683.82       1.000
+    11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
+    12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
+    13 Mainchain Omega dihedral restraints:     260       0      1   3.247   3.247      31.478       1.000
+    14 Sidechain Chi_1 dihedral restraints:     227       0      0  51.888  51.888      7.6842       1.000
+    15 Sidechain Chi_2 dihedral restraints:     169       0      1  64.007  64.007      31.177       1.000
+    16 Sidechain Chi_3 dihedral restraints:      48       0      0  65.360  65.360      28.065       1.000
+    17 Sidechain Chi_4 dihedral restraints:       8       0      0  76.540  76.540      4.6040       1.000
+    18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
+    19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
+    20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
+    21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    23 Distance restraints 3 (SDCH-MNCH)  :    3891       0      0   0.294   0.294      2710.2       1.000
+    24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
+    25 Phi/Psi pair of dihedral restraints:     259       3      9  14.765  19.037     -178.33       1.000
+    26 Distance restraints 4 (SDCH-SDCH)  :    2426       0      5   0.669   0.669      1979.0       1.000
+    27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
+    28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
+    29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
+    30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
+    31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
+    32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
+    34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
+    35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
+    36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
+    37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
+    38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
+    39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000
+    
+    
+    
+    # Heavy relative violation of each residue is written to: 9606_F.V99990001
+    # The profile is NOT normalized by the number of restraints.
+    # The profiles are smoothed over a window of residues:    1
+    # The sum of all numbers in the file:   17361.5898
+    
+    
+    
+    List of the violated restraints:
+       A restraint is violated when the relative difference
+       from the best value (RVIOL) is larger than CUTOFF.
+    
+       ICSR   ... index of a restraint in the current set.
+       RESNO  ... residue numbers of the first two atoms.
+       ATM    ... IUPAC atom names of the first two atoms.
+       FEAT   ... the value of the feature in the model.
+       restr  ... the mean of the basis restraint with the smallest
+                  difference from the model (local minimum).
+       viol   ... difference from the local minimum.
+       rviol  ... relative difference from the local minimum.
+       RESTR  ... the best value (global minimum).
+       VIOL   ... difference from the best value.
+       RVIOL  ... relative difference from the best value.
+    
+    
+    -------------------------------------------------------------------------------------------------
+    
+    Feature 25                           : Phi/Psi pair of dihedral restraints     
+    List of the RVIOL violations larger than   :       6.5000
+    
+        #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
+        1   8020   1M   2T C   N       7    9  -76.22  -78.10    9.41    0.47  -63.20  159.41   21.31
+        1          2T   2T N   CA      9   10  159.02  149.80                  -42.10
+        2   8146 127L 128E C   N    1030 1032  -86.22  -63.60   82.68   12.30  -69.30   99.13    6.96
+        2        128E 128E N   CA   1032 1033 -119.82  -40.30                  142.50
+        3   8250 231H 232H C   N    1855 1857 -112.98  -63.20   78.73    8.57  -63.20   78.73    8.57
+        3        232H 232H N   CA   1857 1858   18.69  -42.30                  -42.30
+    
+    
+    report______> Distribution of short non-bonded contacts:
+    
+    
+    DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
+    DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
+    FREQUENCY:     0    0    0    0    0    5   20   66  185  232  194  296  363  405  376
+    
+    
+    << end of ENERGY.
+    
+    >> Summary of successfully produced models:
+    Filename                          molpdf
+    ----------------------------------------
+    9606_F.B99990001.pdb          6458.98828
+    
+    9606_S
+    automodel__W> Topology and/or parameter libraries already in memory. These will
+                    be used instead of the automodel defaults. If this is not what you
+                    want, clear them before creating the automodel object with
+                    env.libs.topology.clear() and env.libs.parameters.clear()
+    
+    
+    check_ali___> Checking pairwise structural superpositions. 
+    
+    Equivalent CA pairs with distance difference larger than  6.0 angstroms:
+    
+    ALN_POS TMPL1 TMPL2  RID1  RID2  NAM1  NAM2     DIST
+    ----------------------------------------------------
+    END OF TABLE
+    
+    check_ali___> Checking the sequence-structure alignment. 
+    
+    Implied target CA(i)-CA(i+1) distances longer than  8.0 angstroms:
+    
+    ALN_POS  TMPL  RID1  RID2  NAM1  NAM2     DIST
+    ----------------------------------------------
+    END OF TABLE
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16   261
+                  atom names           : C     +N
+                  atom indices         :  2124     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16   261
+                  atom names           : C     CA    +N    O
+                  atom indices         :  2124  2121     0  2125
+    mdtrsr__446W> A potential that relies on one protein is used, yet you have at
+                  least one known structure available. MDT, not library, potential is used.
+    0 atoms in HETATM/BLK residues constrained
+    to protein atoms within 2.30 angstroms
+    and protein CA atoms within 10.00 angstroms
+    0 atoms in residues without defined topology
+    constrained to be rigid bodies
+    condens_443_> Restraints marked for deletion were removed.
+                  Total number of restraints before, now:    26168    24318
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    
+    
+    >> ENERGY; Differences between the model's features and restraints:
+    Number of all residues in MODEL                   :      261
+    Number of all, selected real atoms                :     2126    2126
+    Number of all, selected pseudo atoms              :        0       0
+    Number of all static, selected restraints         :    24318   24318
+    COVALENT_CYS                                      :        F
+    NONBONDED_SEL_ATOMS                               :        1
+    Number of non-bonded pairs (excluding 1-2,1-3,1-4):     4781
+    Dynamic pairs routine                             : 2, NATM x NATM cell sorting
+    Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
+    LENNARD_JONES_SWITCH                              :    6.500   7.500
+    COULOMB_JONES_SWITCH                              :    6.500   7.500
+    RESIDUE_SPAN_RANGE                                :        0   99999
+    NLOGN_USE                                         :       15
+    CONTACT_SHELL                                     :    4.000
+    DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
+    SPHERE_STDV                                       :    0.050
+    RADII_FACTOR                                      :    0.820
+    Current energy                                    :        6496.0596
+    
+    
+    
+    
+    
+    Summary of the restraint violations: 
+    
+       NUM     ... number of restraints.
+       NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
+       RVIOL   ... relative difference from the best value.
+       NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
+       RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
+       RMS_2   ... RMS(feature, best_value, NUMB).
+       MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
+    
+     #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
+    ------------------------------------------------------------------------------------------------------
+     1 Bond length potential              :    2213       0      0   0.004   0.004      10.469       1.000
+     2 Bond angle potential               :    3028       0      3   1.765   1.765      185.98       1.000
+     3 Stereochemical cosine torsion poten:    1705       0     16  38.623  38.623      370.38       1.000
+     4 Stereochemical improper torsion pot:    1044       0      0   0.990   0.990      20.826       1.000
+     5 Soft-sphere overlap restraints     :    4781       0      0   0.001   0.001     0.59371       1.000
+     6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
+     7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
+     8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
+     9 Distance restraints 1 (CA-CA)      :    4433       0      1   0.095   0.095      587.31       1.000
+    10 Distance restraints 2 (N-O)        :    4608       0      0   0.117   0.117      682.60       1.000
+    11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
+    12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
+    13 Mainchain Omega dihedral restraints:     260       0      1   3.238   3.238      31.315       1.000
+    14 Sidechain Chi_1 dihedral restraints:     227       0      0  46.690  46.690      2.9465       1.000
+    15 Sidechain Chi_2 dihedral restraints:     168       0      2  61.521  61.521      38.612       1.000
+    16 Sidechain Chi_3 dihedral restraints:      48       0      0  52.863  52.863      26.667       1.000
+    17 Sidechain Chi_4 dihedral restraints:       8       0      0  99.049  99.049      5.3430       1.000
+    18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
+    19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
+    20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
+    21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    23 Distance restraints 3 (SDCH-MNCH)  :    3891       0      0   0.308   0.308      2711.7       1.000
+    24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
+    25 Phi/Psi pair of dihedral restraints:     259       2     10  15.336  16.194     -173.24       1.000
+    26 Distance restraints 4 (SDCH-SDCH)  :    2426       0      8   0.704   0.704      1994.5       1.000
+    27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
+    28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
+    29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
+    30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
+    31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
+    32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
+    34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
+    35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
+    36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
+    37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
+    38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
+    39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000
+    
+    
+    
+    # Heavy relative violation of each residue is written to: 9606_S.V99990001
+    # The profile is NOT normalized by the number of restraints.
+    # The profiles are smoothed over a window of residues:    1
+    # The sum of all numbers in the file:   16972.8242
+    
+    
+    
+    List of the violated restraints:
+       A restraint is violated when the relative difference
+       from the best value (RVIOL) is larger than CUTOFF.
+    
+       ICSR   ... index of a restraint in the current set.
+       RESNO  ... residue numbers of the first two atoms.
+       ATM    ... IUPAC atom names of the first two atoms.
+       FEAT   ... the value of the feature in the model.
+       restr  ... the mean of the basis restraint with the smallest
+                  difference from the model (local minimum).
+       viol   ... difference from the local minimum.
+       rviol  ... relative difference from the local minimum.
+       RESTR  ... the best value (global minimum).
+       VIOL   ... difference from the best value.
+       RVIOL  ... relative difference from the best value.
+    
+    
+    -------------------------------------------------------------------------------------------------
+    
+    Feature 25                           : Phi/Psi pair of dihedral restraints     
+    List of the RVIOL violations larger than   :       6.5000
+    
+        #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
+        1   8117 127L 128E C   N    1025 1027  -86.68  -63.60   83.76   12.47  -69.30   98.23    6.87
+        1        128E 128E N   CA   1027 1028 -120.82  -40.30                  142.50
+        2   8221 231H 232H C   N    1850 1852 -114.13  -63.20   81.80    8.88  -63.20   81.80    8.88
+        2        232H 232H N   CA   1852 1853   21.72  -42.30                  -42.30
+    
+    
+    report______> Distribution of short non-bonded contacts:
+    
+    
+    DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
+    DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
+    FREQUENCY:     0    0    0    0    0    9   17   61  175  237  197  299  355  418  379
+    
+    
+    << end of ENERGY.
+    
+    >> Summary of successfully produced models:
+    Filename                          molpdf
+    ----------------------------------------
+    9606_S.B99990001.pdb          6496.05957
+    
+    9606_L
+    automodel__W> Topology and/or parameter libraries already in memory. These will
+                    be used instead of the automodel defaults. If this is not what you
+                    want, clear them before creating the automodel object with
+                    env.libs.topology.clear() and env.libs.parameters.clear()
+    
+    
+    check_ali___> Checking pairwise structural superpositions. 
+    
+    Equivalent CA pairs with distance difference larger than  6.0 angstroms:
+    
+    ALN_POS TMPL1 TMPL2  RID1  RID2  NAM1  NAM2     DIST
+    ----------------------------------------------------
+    END OF TABLE
+    
+    check_ali___> Checking the sequence-structure alignment. 
+    
+    Implied target CA(i)-CA(i+1) distances longer than  8.0 angstroms:
+    
+    ALN_POS  TMPL  RID1  RID2  NAM1  NAM2     DIST
+    ----------------------------------------------
+    END OF TABLE
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16   261
+                  atom names           : C     +N
+                  atom indices         :  2126     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16   261
+                  atom names           : C     CA    +N    O
+                  atom indices         :  2126  2123     0  2127
+    mdtrsr__446W> A potential that relies on one protein is used, yet you have at
+                  least one known structure available. MDT, not library, potential is used.
+    0 atoms in HETATM/BLK residues constrained
+    to protein atoms within 2.30 angstroms
+    and protein CA atoms within 10.00 angstroms
+    0 atoms in residues without defined topology
+    constrained to be rigid bodies
+    condens_443_> Restraints marked for deletion were removed.
+                  Total number of restraints before, now:    26177    24326
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    
+    
+    >> ENERGY; Differences between the model's features and restraints:
+    Number of all residues in MODEL                   :      261
+    Number of all, selected real atoms                :     2128    2128
+    Number of all, selected pseudo atoms              :        0       0
+    Number of all static, selected restraints         :    24326   24326
+    COVALENT_CYS                                      :        F
+    NONBONDED_SEL_ATOMS                               :        1
+    Number of non-bonded pairs (excluding 1-2,1-3,1-4):     4822
+    Dynamic pairs routine                             : 2, NATM x NATM cell sorting
+    Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
+    LENNARD_JONES_SWITCH                              :    6.500   7.500
+    COULOMB_JONES_SWITCH                              :    6.500   7.500
+    RESIDUE_SPAN_RANGE                                :        0   99999
+    NLOGN_USE                                         :       15
+    CONTACT_SHELL                                     :    4.000
+    DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
+    SPHERE_STDV                                       :    0.050
+    RADII_FACTOR                                      :    0.820
+    Current energy                                    :        6708.4106
+    
+    
+    
+    
+    
+    Summary of the restraint violations: 
+    
+       NUM     ... number of restraints.
+       NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
+       RVIOL   ... relative difference from the best value.
+       NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
+       RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
+       RMS_2   ... RMS(feature, best_value, NUMB).
+       MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
+    
+     #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
+    ------------------------------------------------------------------------------------------------------
+     1 Bond length potential              :    2215       0      0   0.005   0.005      12.566       1.000
+     2 Bond angle potential               :    3031       0      3   1.867   1.867      206.95       1.000
+     3 Stereochemical cosine torsion poten:    1706       0     18  39.086  39.086      379.94       1.000
+     4 Stereochemical improper torsion pot:    1045       0      0   1.093   1.093      24.881       1.000
+     5 Soft-sphere overlap restraints     :    4822       0      0   0.001   0.001     0.90441       1.000
+     6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
+     7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
+     8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
+     9 Distance restraints 1 (CA-CA)      :    4433       0      2   0.124   0.124      621.07       1.000
+    10 Distance restraints 2 (N-O)        :    4608       0      4   0.143   0.143      723.61       1.000
+    11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
+    12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
+    13 Mainchain Omega dihedral restraints:     260       0      1   3.542   3.542      37.629       1.000
+    14 Sidechain Chi_1 dihedral restraints:     227       0      0  50.898  50.898      15.005       1.000
+    15 Sidechain Chi_2 dihedral restraints:     169       0      1  62.237  62.237      40.949       1.000
+    16 Sidechain Chi_3 dihedral restraints:      48       0      0  67.335  67.335      29.038       1.000
+    17 Sidechain Chi_4 dihedral restraints:       8       0      0  76.220  76.220      6.3086       1.000
+    18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
+    19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
+    20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
+    21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    23 Distance restraints 3 (SDCH-MNCH)  :    3891       0      0   0.335   0.335      2726.8       1.000
+    24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
+    25 Phi/Psi pair of dihedral restraints:     259       7     14  19.300  28.110     -152.14       1.000
+    26 Distance restraints 4 (SDCH-SDCH)  :    2426       0     14   0.775   0.775      2034.9       1.000
+    27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
+    28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
+    29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
+    30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
+    31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
+    32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
+    34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
+    35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
+    36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
+    37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
+    38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
+    39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000
+    
+    
+    
+    # Heavy relative violation of each residue is written to: 9606_L.V99990001
+    # The profile is NOT normalized by the number of restraints.
+    # The profiles are smoothed over a window of residues:    1
+    # The sum of all numbers in the file:   19367.4160
+    
+    
+    
+    List of the violated restraints:
+       A restraint is violated when the relative difference
+       from the best value (RVIOL) is larger than CUTOFF.
+    
+       ICSR   ... index of a restraint in the current set.
+       RESNO  ... residue numbers of the first two atoms.
+       ATM    ... IUPAC atom names of the first two atoms.
+       FEAT   ... the value of the feature in the model.
+       restr  ... the mean of the basis restraint with the smallest
+                  difference from the model (local minimum).
+       viol   ... difference from the local minimum.
+       rviol  ... relative difference from the local minimum.
+       RESTR  ... the best value (global minimum).
+       VIOL   ... difference from the best value.
+       RVIOL  ... relative difference from the best value.
+    
+    
+    -------------------------------------------------------------------------------------------------
+    
+    Feature 25                           : Phi/Psi pair of dihedral restraints     
+    List of the RVIOL violations larger than   :       6.5000
+    
+        #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
+        1   7998   1M   2T C   N       7    9  -80.00  -78.10    7.10    0.25  -63.20  162.13   21.91
+        1          2T   2T N   CA      9   10  156.64  149.80                  -42.10
+        2   8007  10M  11V C   N      84   86  -63.70  -62.40    2.01    0.23  -73.50 -179.80   15.52
+        2         11V  11V N   CA     86   87  -40.87  -42.40                  139.20
+        3   8008  11V  12K C   N      91   93   84.34  -70.20  154.84   11.07  -70.20  154.84   11.07
+        3         12K  12K N   CA     93   94  130.79  140.40                  140.40
+        4   8119 122T 123P C   N     989  991  -57.88  -58.70   24.55    1.96  -64.50  157.91   12.14
+        4        123P 123P N   CA    991  992  -55.03  -30.50                  147.20
+        5   8120 123P 124L C   N     996  998  126.04 -108.50  125.73    5.89  -70.70  163.26   14.87
+        5        124L 124L N   CA    998  999  140.81  132.50                  141.60
+        6   8124 127L 128E C   N    1027 1029  -87.12  -63.60   81.35   12.18  -69.30  100.90    7.06
+        6        128E 128E N   CA   1029 1030 -118.18  -40.30                  142.50
+        7   8228 231H 232H C   N    1852 1854 -113.64  -63.20   79.29    8.64  -63.20   79.29    8.64
+        7        232H 232H N   CA   1854 1855   18.87  -42.30                  -42.30
+    
+    
+    report______> Distribution of short non-bonded contacts:
+    
+    
+    DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
+    DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
+    FREQUENCY:     0    0    0    0    0    8   15   81  183  233  198  284  381  403  371
+    
+    
+    << end of ENERGY.
+    
+    >> Summary of successfully produced models:
+    Filename                          molpdf
+    ----------------------------------------
+    9606_L.B99990001.pdb          6708.41064
+    
+    9606_M
+    automodel__W> Topology and/or parameter libraries already in memory. These will
+                    be used instead of the automodel defaults. If this is not what you
+                    want, clear them before creating the automodel object with
+                    env.libs.topology.clear() and env.libs.parameters.clear()
+    
+    
+    check_ali___> Checking pairwise structural superpositions. 
+    
+    Equivalent CA pairs with distance difference larger than  6.0 angstroms:
+    
+    ALN_POS TMPL1 TMPL2  RID1  RID2  NAM1  NAM2     DIST
+    ----------------------------------------------------
+    END OF TABLE
+    
+    check_ali___> Checking the sequence-structure alignment. 
+    
+    Implied target CA(i)-CA(i+1) distances longer than  8.0 angstroms:
+    
+    ALN_POS  TMPL  RID1  RID2  NAM1  NAM2     DIST
+    ----------------------------------------------
+    END OF TABLE
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16   261
+                  atom names           : C     +N
+                  atom indices         :  2126     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16   261
+                  atom names           : C     CA    +N    O
+                  atom indices         :  2126  2123     0  2127
+    mdtrsr__446W> A potential that relies on one protein is used, yet you have at
+                  least one known structure available. MDT, not library, potential is used.
+    0 atoms in HETATM/BLK residues constrained
+    to protein atoms within 2.30 angstroms
+    and protein CA atoms within 10.00 angstroms
+    0 atoms in residues without defined topology
+    constrained to be rigid bodies
+    condens_443_> Restraints marked for deletion were removed.
+                  Total number of restraints before, now:    26177    24324
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    
+    
+    >> ENERGY; Differences between the model's features and restraints:
+    Number of all residues in MODEL                   :      261
+    Number of all, selected real atoms                :     2128    2128
+    Number of all, selected pseudo atoms              :        0       0
+    Number of all static, selected restraints         :    24324   24324
+    COVALENT_CYS                                      :        F
+    NONBONDED_SEL_ATOMS                               :        1
+    Number of non-bonded pairs (excluding 1-2,1-3,1-4):     4830
+    Dynamic pairs routine                             : 2, NATM x NATM cell sorting
+    Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
+    LENNARD_JONES_SWITCH                              :    6.500   7.500
+    COULOMB_JONES_SWITCH                              :    6.500   7.500
+    RESIDUE_SPAN_RANGE                                :        0   99999
+    NLOGN_USE                                         :       15
+    CONTACT_SHELL                                     :    4.000
+    DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
+    SPHERE_STDV                                       :    0.050
+    RADII_FACTOR                                      :    0.820
+    Current energy                                    :        6481.8320
+    
+    
+    
+    
+    
+    Summary of the restraint violations: 
+    
+       NUM     ... number of restraints.
+       NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
+       RVIOL   ... relative difference from the best value.
+       NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
+       RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
+       RMS_2   ... RMS(feature, best_value, NUMB).
+       MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
+    
+     #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
+    ------------------------------------------------------------------------------------------------------
+     1 Bond length potential              :    2215       0      0   0.004   0.004      10.731       1.000
+     2 Bond angle potential               :    3030       0      3   1.777   1.777      188.35       1.000
+     3 Stereochemical cosine torsion poten:    1705       0     16  38.765  38.765      371.22       1.000
+     4 Stereochemical improper torsion pot:    1044       0      0   1.009   1.009      21.571       1.000
+     5 Soft-sphere overlap restraints     :    4830       0      0   0.001   0.001     0.79378       1.000
+     6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
+     7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
+     8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
+     9 Distance restraints 1 (CA-CA)      :    4433       0      0   0.088   0.088      582.13       1.000
+    10 Distance restraints 2 (N-O)        :    4608       0      0   0.118   0.118      684.87       1.000
+    11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
+    12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
+    13 Mainchain Omega dihedral restraints:     260       0      1   3.280   3.280      32.136       1.000
+    14 Sidechain Chi_1 dihedral restraints:     227       0      1  51.328  51.328      10.403       1.000
+    15 Sidechain Chi_2 dihedral restraints:     169       0      1  60.299  60.299      30.779       1.000
+    16 Sidechain Chi_3 dihedral restraints:      49       0      0  66.051  66.051      29.338       1.000
+    17 Sidechain Chi_4 dihedral restraints:       8       0      0  86.862  86.862      5.4540       1.000
+    18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
+    19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
+    20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
+    21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    23 Distance restraints 3 (SDCH-MNCH)  :    3891       0      0   0.318   0.318      2721.0       1.000
+    24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
+    25 Phi/Psi pair of dihedral restraints:     259       3      8  14.925  19.469     -174.50       1.000
+    26 Distance restraints 4 (SDCH-SDCH)  :    2426       0      8   0.647   0.647      1967.6       1.000
+    27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
+    28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
+    29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
+    30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
+    31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
+    32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
+    34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
+    35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
+    36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
+    37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
+    38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
+    39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000
+    
+    
+    
+    # Heavy relative violation of each residue is written to: 9606_M.V99990001
+    # The profile is NOT normalized by the number of restraints.
+    # The profiles are smoothed over a window of residues:    1
+    # The sum of all numbers in the file:   17671.6875
+    
+    
+    
+    List of the violated restraints:
+       A restraint is violated when the relative difference
+       from the best value (RVIOL) is larger than CUTOFF.
+    
+       ICSR   ... index of a restraint in the current set.
+       RESNO  ... residue numbers of the first two atoms.
+       ATM    ... IUPAC atom names of the first two atoms.
+       FEAT   ... the value of the feature in the model.
+       restr  ... the mean of the basis restraint with the smallest
+                  difference from the model (local minimum).
+       viol   ... difference from the local minimum.
+       rviol  ... relative difference from the local minimum.
+       RESTR  ... the best value (global minimum).
+       VIOL   ... difference from the best value.
+       RVIOL  ... relative difference from the best value.
+    
+    
+    -------------------------------------------------------------------------------------------------
+    
+    Feature 25                           : Phi/Psi pair of dihedral restraints     
+    List of the RVIOL violations larger than   :       6.5000
+    
+        #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
+        1   7995   1M   2T C   N       7    9 -118.91 -124.80   11.30    0.35  -63.20 -175.43   20.51
+        1          2T   2T N   CA      9   10  133.86  143.50                  -42.10
+        2   8121 127L 128E C   N    1027 1029  -84.52  -63.60   86.20   12.68  -69.30   94.80    6.69
+        2        128E 128E N   CA   1029 1030 -123.93  -40.30                  142.50
+        3   8225 231H 232H C   N    1852 1854 -113.35  -63.20   79.68    8.67  -63.20   79.68    8.67
+        3        232H 232H N   CA   1854 1855   19.62  -42.30                  -42.30
+    
+    
+    report______> Distribution of short non-bonded contacts:
+    
+    
+    DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
+    DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
+    FREQUENCY:     0    0    0    0    0   12   19   68  185  260  187  275  353  408  393
+    
+    
+    << end of ENERGY.
+    
+    >> Summary of successfully produced models:
+    Filename                          molpdf
+    ----------------------------------------
+    9606_M.B99990001.pdb          6481.83203
+    
+    9606_E
+    automodel__W> Topology and/or parameter libraries already in memory. These will
+                    be used instead of the automodel defaults. If this is not what you
+                    want, clear them before creating the automodel object with
+                    env.libs.topology.clear() and env.libs.parameters.clear()
+    
+    
+    check_ali___> Checking pairwise structural superpositions. 
+    
+    Equivalent CA pairs with distance difference larger than  6.0 angstroms:
+    
+    ALN_POS TMPL1 TMPL2  RID1  RID2  NAM1  NAM2     DIST
+    ----------------------------------------------------
+    END OF TABLE
+    
+    check_ali___> Checking the sequence-structure alignment. 
+    
+    Implied target CA(i)-CA(i+1) distances longer than  8.0 angstroms:
+    
+    ALN_POS  TMPL  RID1  RID2  NAM1  NAM2     DIST
+    ----------------------------------------------
+    END OF TABLE
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16   261
+                  atom names           : C     +N
+                  atom indices         :  2127     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16   261
+                  atom names           : C     CA    +N    O
+                  atom indices         :  2127  2124     0  2128
+    mdtrsr__446W> A potential that relies on one protein is used, yet you have at
+                  least one known structure available. MDT, not library, potential is used.
+    0 atoms in HETATM/BLK residues constrained
+    to protein atoms within 2.30 angstroms
+    and protein CA atoms within 10.00 angstroms
+    0 atoms in residues without defined topology
+    constrained to be rigid bodies
+    condens_443_> Restraints marked for deletion were removed.
+                  Total number of restraints before, now:    26181    24329
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    
+    
+    >> ENERGY; Differences between the model's features and restraints:
+    Number of all residues in MODEL                   :      261
+    Number of all, selected real atoms                :     2129    2129
+    Number of all, selected pseudo atoms              :        0       0
+    Number of all static, selected restraints         :    24329   24329
+    COVALENT_CYS                                      :        F
+    NONBONDED_SEL_ATOMS                               :        1
+    Number of non-bonded pairs (excluding 1-2,1-3,1-4):     4776
+    Dynamic pairs routine                             : 2, NATM x NATM cell sorting
+    Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
+    LENNARD_JONES_SWITCH                              :    6.500   7.500
+    COULOMB_JONES_SWITCH                              :    6.500   7.500
+    RESIDUE_SPAN_RANGE                                :        0   99999
+    NLOGN_USE                                         :       15
+    CONTACT_SHELL                                     :    4.000
+    DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
+    SPHERE_STDV                                       :    0.050
+    RADII_FACTOR                                      :    0.820
+    Current energy                                    :        6525.7900
+    
+    
+    
+    
+    
+    Summary of the restraint violations: 
+    
+       NUM     ... number of restraints.
+       NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
+       RVIOL   ... relative difference from the best value.
+       NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
+       RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
+       RMS_2   ... RMS(feature, best_value, NUMB).
+       MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
+    
+     #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
+    ------------------------------------------------------------------------------------------------------
+     1 Bond length potential              :    2216       0      0   0.004   0.004      11.308       1.000
+     2 Bond angle potential               :    3032       0      3   1.798   1.798      194.33       1.000
+     3 Stereochemical cosine torsion poten:    1706       0     18  38.780  38.780      372.87       1.000
+     4 Stereochemical improper torsion pot:    1045       0      0   1.055   1.055      23.452       1.000
+     5 Soft-sphere overlap restraints     :    4776       0      0   0.001   0.001     0.93099       1.000
+     6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
+     7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
+     8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
+     9 Distance restraints 1 (CA-CA)      :    4433       0      0   0.105   0.105      597.93       1.000
+    10 Distance restraints 2 (N-O)        :    4608       0      0   0.126   0.126      694.13       1.000
+    11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
+    12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
+    13 Mainchain Omega dihedral restraints:     260       0      1   3.414   3.414      34.899       1.000
+    14 Sidechain Chi_1 dihedral restraints:     227       0      0  48.551  48.551      12.009       1.000
+    15 Sidechain Chi_2 dihedral restraints:     169       0      1  55.942  55.942      31.060       1.000
+    16 Sidechain Chi_3 dihedral restraints:      49       0      0  58.473  58.473      27.663       1.000
+    17 Sidechain Chi_4 dihedral restraints:       8       0      0 104.502 104.502      4.9916       1.000
+    18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
+    19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
+    20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
+    21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    23 Distance restraints 3 (SDCH-MNCH)  :    3891       0      0   0.307   0.307      2713.5       1.000
+    24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
+    25 Phi/Psi pair of dihedral restraints:     259       5     10  17.664  24.563     -164.98       1.000
+    26 Distance restraints 4 (SDCH-SDCH)  :    2426       0      4   0.652   0.652      1971.7       1.000
+    27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
+    28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
+    29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
+    30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
+    31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
+    32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
+    34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
+    35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
+    36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
+    37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
+    38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
+    39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000
+    
+    
+    
+    # Heavy relative violation of each residue is written to: 9606_E.V99990001
+    # The profile is NOT normalized by the number of restraints.
+    # The profiles are smoothed over a window of residues:    1
+    # The sum of all numbers in the file:   17560.6973
+    
+    
+    
+    List of the violated restraints:
+       A restraint is violated when the relative difference
+       from the best value (RVIOL) is larger than CUTOFF.
+    
+       ICSR   ... index of a restraint in the current set.
+       RESNO  ... residue numbers of the first two atoms.
+       ATM    ... IUPAC atom names of the first two atoms.
+       FEAT   ... the value of the feature in the model.
+       restr  ... the mean of the basis restraint with the smallest
+                  difference from the model (local minimum).
+       viol   ... difference from the local minimum.
+       rviol  ... relative difference from the local minimum.
+       RESTR  ... the best value (global minimum).
+       VIOL   ... difference from the best value.
+       RVIOL  ... relative difference from the best value.
+    
+    
+    -------------------------------------------------------------------------------------------------
+    
+    Feature 25                           : Phi/Psi pair of dihedral restraints     
+    List of the RVIOL violations larger than   :       6.5000
+    
+        #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
+        1   8000   1M   2T C   N       7    9  -75.07  -78.10   15.73    0.58  -63.20  176.86   21.92
+        1          2T   2T N   CA      9   10  134.36  149.80                  -42.10
+        2   8009  10M  11V C   N      84   86  -64.17  -62.40    1.80    0.30  -73.50  178.32   15.36
+        2         11V  11V N   CA     86   87  -42.72  -42.40                  139.20
+        3   8010  11V  12K C   N      91   93   90.81 -118.00  151.52    5.89  -70.20  161.40   11.51
+        3         12K  12K N   CA     93   94  129.07  139.10                  140.40
+        4   8126 127L 128E C   N    1028 1030  -85.27  -63.60   84.15   12.45  -69.30   97.21    6.85
+        4        128E 128E N   CA   1030 1031 -121.61  -40.30                  142.50
+        5   8230 231H 232H C   N    1853 1855 -113.24  -63.20   78.26    8.54  -63.20   78.26    8.54
+        5        232H 232H N   CA   1855 1856   17.86  -42.30                  -42.30
+    
+    
+    report______> Distribution of short non-bonded contacts:
+    
+    
+    DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
+    DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
+    FREQUENCY:     0    0    0    0    0   11   16   63  193  239  209  270  378  398  347
+    
+    
+    << end of ENERGY.
+    
+    >> Summary of successfully produced models:
+    Filename                          molpdf
+    ----------------------------------------
+    9606_E.B99990001.pdb          6525.79004
+    
+    9606_T
+    automodel__W> Topology and/or parameter libraries already in memory. These will
+                    be used instead of the automodel defaults. If this is not what you
+                    want, clear them before creating the automodel object with
+                    env.libs.topology.clear() and env.libs.parameters.clear()
+    
+    
+    check_ali___> Checking pairwise structural superpositions. 
+    
+    Equivalent CA pairs with distance difference larger than  6.0 angstroms:
+    
+    ALN_POS TMPL1 TMPL2  RID1  RID2  NAM1  NAM2     DIST
+    ----------------------------------------------------
+    END OF TABLE
+    
+    check_ali___> Checking the sequence-structure alignment. 
+    
+    Implied target CA(i)-CA(i+1) distances longer than  8.0 angstroms:
+    
+    ALN_POS  TMPL  RID1  RID2  NAM1  NAM2     DIST
+    ----------------------------------------------
+    END OF TABLE
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16   261
+                  atom names           : C     +N
+                  atom indices         :  2125     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16   261
+                  atom names           : C     CA    +N    O
+                  atom indices         :  2125  2122     0  2126
+    mdtrsr__446W> A potential that relies on one protein is used, yet you have at
+                  least one known structure available. MDT, not library, potential is used.
+    0 atoms in HETATM/BLK residues constrained
+    to protein atoms within 2.30 angstroms
+    and protein CA atoms within 10.00 angstroms
+    0 atoms in residues without defined topology
+    constrained to be rigid bodies
+    condens_443_> Restraints marked for deletion were removed.
+                  Total number of restraints before, now:    26174    24324
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    
+    
+    >> ENERGY; Differences between the model's features and restraints:
+    Number of all residues in MODEL                   :      261
+    Number of all, selected real atoms                :     2127    2127
+    Number of all, selected pseudo atoms              :        0       0
+    Number of all static, selected restraints         :    24324   24324
+    COVALENT_CYS                                      :        F
+    NONBONDED_SEL_ATOMS                               :        1
+    Number of non-bonded pairs (excluding 1-2,1-3,1-4):     4799
+    Dynamic pairs routine                             : 2, NATM x NATM cell sorting
+    Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
+    LENNARD_JONES_SWITCH                              :    6.500   7.500
+    COULOMB_JONES_SWITCH                              :    6.500   7.500
+    RESIDUE_SPAN_RANGE                                :        0   99999
+    NLOGN_USE                                         :       15
+    CONTACT_SHELL                                     :    4.000
+    DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
+    SPHERE_STDV                                       :    0.050
+    RADII_FACTOR                                      :    0.820
+    Current energy                                    :        6491.0776
+    
+    
+    
+    
+    
+    Summary of the restraint violations: 
+    
+       NUM     ... number of restraints.
+       NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
+       RVIOL   ... relative difference from the best value.
+       NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
+       RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
+       RMS_2   ... RMS(feature, best_value, NUMB).
+       MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
+    
+     #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
+    ------------------------------------------------------------------------------------------------------
+     1 Bond length potential              :    2214       0      0   0.004   0.004      10.739       1.000
+     2 Bond angle potential               :    3030       0      3   1.772   1.772      188.93       1.000
+     3 Stereochemical cosine torsion poten:    1707       0     16  38.673  38.673      373.66       1.000
+     4 Stereochemical improper torsion pot:    1045       0      0   1.005   1.005      21.394       1.000
+     5 Soft-sphere overlap restraints     :    4799       0      0   0.001   0.001     0.85217       1.000
+     6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
+     7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
+     8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
+     9 Distance restraints 1 (CA-CA)      :    4433       0      0   0.093   0.093      587.81       1.000
+    10 Distance restraints 2 (N-O)        :    4608       0      0   0.123   0.123      692.58       1.000
+    11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
+    12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
+    13 Mainchain Omega dihedral restraints:     260       0      2   3.344   3.344      33.443       1.000
+    14 Sidechain Chi_1 dihedral restraints:     227       0      1  45.689  45.689      2.8490       1.000
+    15 Sidechain Chi_2 dihedral restraints:     168       0      1  61.520  61.520      35.658       1.000
+    16 Sidechain Chi_3 dihedral restraints:      48       0      0  67.905  67.905      29.969       1.000
+    17 Sidechain Chi_4 dihedral restraints:       8       0      0  99.536  99.536      6.2528       1.000
+    18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
+    19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
+    20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
+    21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    23 Distance restraints 3 (SDCH-MNCH)  :    3891       0      0   0.295   0.295      2711.0       1.000
+    24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
+    25 Phi/Psi pair of dihedral restraints:     259       5     10  17.714  23.571     -167.37       1.000
+    26 Distance restraints 4 (SDCH-SDCH)  :    2426       0      8   0.636   0.636      1963.3       1.000
+    27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
+    28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
+    29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
+    30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
+    31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
+    32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
+    34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
+    35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
+    36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
+    37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
+    38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
+    39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000
+    
+    
+    
+    # Heavy relative violation of each residue is written to: 9606_T.V99990001
+    # The profile is NOT normalized by the number of restraints.
+    # The profiles are smoothed over a window of residues:    1
+    # The sum of all numbers in the file:   17342.1797
+    
+    
+    
+    List of the violated restraints:
+       A restraint is violated when the relative difference
+       from the best value (RVIOL) is larger than CUTOFF.
+    
+       ICSR   ... index of a restraint in the current set.
+       RESNO  ... residue numbers of the first two atoms.
+       ATM    ... IUPAC atom names of the first two atoms.
+       FEAT   ... the value of the feature in the model.
+       restr  ... the mean of the basis restraint with the smallest
+                  difference from the model (local minimum).
+       viol   ... difference from the local minimum.
+       rviol  ... relative difference from the local minimum.
+       RESTR  ... the best value (global minimum).
+       VIOL   ... difference from the best value.
+       RVIOL  ... relative difference from the best value.
+    
+    
+    -------------------------------------------------------------------------------------------------
+    
+    Feature 25                           : Phi/Psi pair of dihedral restraints     
+    List of the RVIOL violations larger than   :       6.5000
+    
+        #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
+        1   7997   1M   2T C   N       7    9  -87.71  -78.10   36.56    1.29  -63.20  135.07   18.96
+        1          2T   2T N   CA      9   10 -174.93  149.80                  -42.10
+        2   8006  10M  11V C   N      84   86  -63.39  -62.40    1.21    0.15  -73.50  179.37   15.46
+        2         11V  11V N   CA     86   87  -41.72  -42.40                  139.20
+        3   8007  11V  12K C   N      91   93   93.97 -118.00  148.04    5.62  -70.20  164.20   11.91
+        3         12K  12K N   CA     93   94  137.03  139.10                  140.40
+        4   8123 127L 128E C   N    1026 1028  -80.18  -63.60   88.05   12.67  -69.30   91.37    6.59
+        4        128E 128E N   CA   1028 1029 -126.78  -40.30                  142.50
+        5   8227 231H 232H C   N    1851 1853 -114.00  -63.20   79.02    8.64  -63.20   79.02    8.64
+        5        232H 232H N   CA   1853 1854   18.23  -42.30                  -42.30
+    
+    
+    report______> Distribution of short non-bonded contacts:
+    
+    
+    DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
+    DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
+    FREQUENCY:     0    0    0    0    0    7   18   66  184  242  213  284  362  395  365
+    
+    
+    << end of ENERGY.
+    
+    >> Summary of successfully produced models:
+    Filename                          molpdf
+    ----------------------------------------
+    9606_T.B99990001.pdb          6491.07764
+    
+
+
+
+```python
+text = 'load 1v55.pdb\nsel 2save, byres(n. ca) and not c. C+P\n'
+for s in aln[:-2]:
+    text+='load out/%s.B99990001.pdb,aa\n' % s.code
+    text+='load out/%s.B99990001.pdb,bb\n' % s.code
+    text+='super aa, C//\n'
+    text+='super bb, P//\n'
+    text+='''alter aa, chain='5'\n'''
+    text+='''alter bb, chain='6'\n'''
+    text+='save mod/%s.pdb, 2save or aa or bb\n' %s.code
+    text+='delete aa or bb\n'
+fl=open('make_mods.pml','w')
+print fl.write(text)
+fl.close()
+```
+
+    None
+
+
+
+```python
+class mymodel(modeller.automodel.automodel):
+    def special_restraints(self, aln):
+        rsr = self.restraints
+        for ids in (('OD1:98:A', 'O6A:131:A'),
+                    ('N:65:A', 'O7B:132:A'),
+                    ('OD2:73:A', 'O1C:133:A')):
+                    atoms = [self.atoms[i] for i in ids]
+                    rsr.add(forms.upper_bound(group=physical.upper_distance,
+                      feature=features.distance(*atoms), mean=3.5, stdev=0.1)) 
+```
+
+
+```python
+mod = modeller.model(env, file='1v55.pdb')
+```
+
+
+```python
+chains=['A','B','C','D','E','F','G','H','I','J','K','L','M']
+accs='''P00395
+P00403
+P00414
+P13073
+Q96KJ9
+P20674
+P10606
+P09669
+P24311
+P15954
+O14548
+O60397
+P10176
+Q7Z4L0
+P12074
+Q02221
+P14854
+Q6YFQ2
+P24310
+P14406'''.split('\n')
+```
+
+
+```python
+mods=[]
+result={}
+text='='*60+'\n'
+for c in chains:
+    pdbname=''
+    m = modeller.model(env, file='1v55.pdb', model_segment=('FIRST:'+c, 'LAST:'+c))
+    names=m.name.split('EC  1.9.3.1;')
+    for n in names:
+        c1 = 'CHAIN  '+c
+        if c1 in n:
+            pdbname= n+'\n'
+    ident={}
+    
+    for ac in accs:
+        a=modeller.alignment(env)
+        a.append(file='seq/'+ac+'.fasta', align_codes='all',alignment_format='FASTA')
+        a.append_model(m, atom_files='1v55.pdb', align_codes='1v55_'+c)
+        a.salign()
+        ident[ac]=a[1].get_sequence_identity(a[0]) 
+        
+    
+    top=sorted(ident, key=ident.get , reverse=True)[0]
+    result[c]=top
+ 
+        
+        
+```
+
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+    
+    SALIGN_____> adding the next group to the alignment; iteration    1
+
+
+
+```python
+%%bash
+cat seq/uni_ids
+cat seq/_how_to
+```
+
+    COX1_HUMAN
+    COX2_HUMAN
+    COX3_HUMAN
+    COX41_HUMAN
+    COX42_HUMAN
+    COX5A_HUMAN
+    COX5B_HUMAN
+    CX6A1_HUMAN
+    CX6A2_HUMAN
+    CX6B1_HUMAN 
+    CX6B2_HUMAN 
+    COX6C_HUMAN
+    CX7A1_HUMAN
+    CX7A2_HUMAN
+    COX7S_HUMAN
+    COX7B_HUMAN
+    COX7C_HUMAN
+    COX7R_HUMAN
+    COX8A_HUMAN
+    COX8C_HUMAN
+    
+    
+    cat uni_ids | parallel --gnu "wget http://www.uniprot.org/uniprot/?query={1}\&sort=score\&columns=id\&format=tab -O {1}.txt"
+    cat  C*txt | grep -v Ent > uni_acc
+    cat uni_acc | parallel --gnu "wget http://www.uniprot.org/uniprot/{1}.fasta"
+    
+
+
+
+```python
+from Bio import pairwise2
+from Bio import SeqIO
+from Bio.SubsMat import MatrixInfo as matlist
+matrix = matlist.blosum62
+gap_open = -10
+gap_extend = -5.50
+```
+
+
+```python
+alighs={}
+struct=''
+models=''
+for c in chains:
+    m = modeller.model(env, file='1v55.pdb', model_segment=('FIRST:'+c, 'LAST:'+c))
+    mseq=''.join(map(lambda x: x.code, m.residues))
+    seq=SeqIO.read('seq/'+result[c]+'.fasta','fasta')
+    alns = pairwise2.align.globalds(mseq, seq.seq.tostring() , matrix, gap_open, gap_extend)
+    a_mseq, a_seq, score, begin, end = alns[0]
+    #print '>%s-%s %s\n%s\n%s\n' % (c,result[c],score, a_mseq,a_seq)
+        #print a_mseq+'\n'+a_seq
+    struct+=a_mseq+'/\n'
+    models+=a_seq+'/\n'
+    #break
+
+
+print '>P1;1v55_P \nstructureX:1v55.pdb:    :A: :M:: 1.90: 0.20'
+print struct+struct[:-2]+'*'
+print '>P1;9913\nsequence::     : :     : :::-1.00:-1.00'
+print models+models[:-2]+'*'
+```
+
+    >P1;1v55_P 
+    structureX:1v55.pdb:    :A: :M:: 1.90: 0.20
+    -FINRWLFSTNHKDIGTLYLLFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLLASSMVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAMSQYQTPLFVWSVMITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIVTYYSGKKEPFGYMGMVWAMMSIGFLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAIPTGVKVFSWLATLHGGNIKWSPAMMWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFVHWFPLFSGYTLNDTWAKIHFAIMFVGVNMTFFPQHFLGLSGMPRRYSDYPDAYTMWNTISSMGSFISLTAVMLMVFIIWEAFASKREVLTVDLTTTNLEWLNGCPPPYHTFEEPTYVNLK/
+    -AYPMQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETIWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLSFDSYMIPTSELKPGELRLLEVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMSSRPGLYYGQCSEICGSNHSFMPIVLELVPLKYFEKWSASML/
+    --HQTHAYHMVNPSPWPLTGALSALLMTSGLTMWFHFNSMTLLMIGLTTNMLTMYQWWRDVIRESTFQGHHTPAVQKGLRYGMILFIISEVLFFTGFFWAFYHSSLAPTPELGGCWPPTGIHPLNPLEVPLLNTSVLLASGVSITWAHHSLMEGDRKHMLQALFITITLGVYFTLLQASEYYEAPFTISDGVYGSTFFVATGFHGLHVIIGSTFLIVCFFRQLKFHFTSNHHFGFEAAAWYWHFVDVVWLFLYVSIYWWGS/
+    -------------------------SVVKSEDYALPSYVDRRDYPLPDVAHVKNLSASQKALKEKEKASWSSLSIDEKVELYRLKFKESFAEMNRSTNEWKTVVGAAMFFIGFTALLLIWEKHYVYGPIPHTFEEEWVAKQTKRMLDMKVAPIQGFSAKWDYDKNEWKK/
+    ------------------------------------------H---ETDEEFDARWVTYFNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVIQELRPTLNELGISTPEELGLDKV/
+    -------------------------------ASGGGVPTDEEQATGLEREVMLAARKGQDPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEAQRCPSCGTHYKLVPHQLAH/
+    ------------ASAAKGDHGG-GARTWRFLTFGLALPSVALCTLNSWLHSGHRERPAFIPYHHLRIRTKPFSWGDGNHTFFHNPRVNPLPTGYEK-/
+    -------KIKNYQTAPFDSRFPNQNQTRNCWQNYLDFHRCEKAMTAKGGDVSVCEWYRRVYKSLCPISWVSTWDDRRAEGTFPGKI/
+    TA---LAKPQMRGLLARRLRFHIVGAFMVSLGFATFYKFAVAEKRKKAYADFYRNYDSMKDFEEMRKAGIFQSAK/
+    ---------------------FENRVAEKQKLFQEDNGLPVHLKGGATDNILYRVTMTLCLGGTLYSLYCLGWASFPHK/
+    -----------------------------APDFHDKYGNAVLASGATFCVAVWVYMATQIGIEWNPSPVGRVTPKEWR--/
+    -----------------HYEEGPGKNIPFSVENKWRLLAMMTLFFGSGFAAPFFIVRHQLLKK/
+    -----------IT--AK----P-AKTPTSP---K----EQAIGLSVTFLSFLLPAGWVLYHLDNYKK-S/
+    -FINRWLFSTNHKDIGTLYLLFGAWAGMVGTALSLLIRAELGQPGTLLGDDQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSFLLLLASSMVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAMSQYQTPLFVWSVMITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIVTYYSGKKEPFGYMGMVWAMMSIGFLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAIPTGVKVFSWLATLHGGNIKWSPAMMWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFVHWFPLFSGYTLNDTWAKIHFAIMFVGVNMTFFPQHFLGLSGMPRRYSDYPDAYTMWNTISSMGSFISLTAVMLMVFIIWEAFASKREVLTVDLTTTNLEWLNGCPPPYHTFEEPTYVNLK/
+    -AYPMQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETIWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLSFDSYMIPTSELKPGELRLLEVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMSSRPGLYYGQCSEICGSNHSFMPIVLELVPLKYFEKWSASML/
+    --HQTHAYHMVNPSPWPLTGALSALLMTSGLTMWFHFNSMTLLMIGLTTNMLTMYQWWRDVIRESTFQGHHTPAVQKGLRYGMILFIISEVLFFTGFFWAFYHSSLAPTPELGGCWPPTGIHPLNPLEVPLLNTSVLLASGVSITWAHHSLMEGDRKHMLQALFITITLGVYFTLLQASEYYEAPFTISDGVYGSTFFVATGFHGLHVIIGSTFLIVCFFRQLKFHFTSNHHFGFEAAAWYWHFVDVVWLFLYVSIYWWGS/
+    -------------------------SVVKSEDYALPSYVDRRDYPLPDVAHVKNLSASQKALKEKEKASWSSLSIDEKVELYRLKFKESFAEMNRSTNEWKTVVGAAMFFIGFTALLLIWEKHYVYGPIPHTFEEEWVAKQTKRMLDMKVAPIQGFSAKWDYDKNEWKK/
+    ------------------------------------------H---ETDEEFDARWVTYFNKPDIDAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVIQELRPTLNELGISTPEELGLDKV/
+    -------------------------------ASGGGVPTDEEQATGLEREVMLAARKGQDPYNILAPKATSGTKEDPNLVPSITNKRIVGCICEEDNSTVIWFWLHKGEAQRCPSCGTHYKLVPHQLAH/
+    ------------ASAAKGDHGG-GARTWRFLTFGLALPSVALCTLNSWLHSGHRERPAFIPYHHLRIRTKPFSWGDGNHTFFHNPRVNPLPTGYEK-/
+    -------KIKNYQTAPFDSRFPNQNQTRNCWQNYLDFHRCEKAMTAKGGDVSVCEWYRRVYKSLCPISWVSTWDDRRAEGTFPGKI/
+    TA---LAKPQMRGLLARRLRFHIVGAFMVSLGFATFYKFAVAEKRKKAYADFYRNYDSMKDFEEMRKAGIFQSAK/
+    ---------------------FENRVAEKQKLFQEDNGLPVHLKGGATDNILYRVTMTLCLGGTLYSLYCLGWASFPHK/
+    -----------------------------APDFHDKYGNAVLASGATFCVAVWVYMATQIGIEWNPSPVGRVTPKEWR--/
+    -----------------HYEEGPGKNIPFSVENKWRLLAMMTLFFGSGFAAPFFIVRHQLLKK/
+    -----------IT--AK----P-AKTPTSP---K----EQAIGLSVTFLSFLLPAGWVLYHLDNYKK-S*
+    >P1;9913
+    sequence::     : :     : :::-1.00:-1.00
+    MFADRWLFSTNHKDIGTLYLLFGAWAGVLGTALSLLIRAELGQPGNLLGNDHIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSLLLLLASAMVEAGAGTGWTVYPPLAGNYSHPGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAMTQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIVTYYSGKKEPFGYMGMVWAMMSIGFLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAIPTGVKVFSWLATLHGSNMKWSAAVLWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFIHWFPLFSGYTLDQTYAKIHFTIMFIGVNLTFFPQHFLGLSGMPRRYSDYPDAYTTWNILSSVGSFISLTAVMLMIFMIWEAFASKRKVLMVEEPSMNLEWLYGCPPPYHTFEEPVYMK-S/
+    MAHAAQVGLQDATSPIMEELITFHDHALMIIFLICFLVLYALFLTLTTKLTNTNISDAQEMETVWTILPAIILVLIALPSLRILYMTDEVNDPSLTIKSIGHQWYWTYEYTDYGGLIFNSYMLPPLFLEPGDLRLLDVDNRVVLPIEAPIRMMITSQDVLHSWAVPTLGLKTDAIPGRLNQTTFTATRPGVYYGQCSEICGANHSFMPIVLELIPLKIFEMGPVFTL/
+    MTHQSHAYHMVKPSPWPLTGALSALLMTSGLAMWFHFHSMTLLMLGLLTNTLTMYQWWRDVTRESTYQGHHTPPVQKGLRYGMILFITSEVFFFAGFFWAFYHSSLAPTPQLGGHWPPTGITPLNPLEVPLLNTSVLLASGVSITWAHHSLMENNRNQMIQALLITILLGLYFTLLQASEYFESPFTISDGIYGSTFFVATGFHGLHVIIGSTFLTICFIRQLMFHFTSKHHFGFEAAAWYWHFVDVVWLFLYVSIYWWGS/
+    MLATRVFSLVGKRAISTSVCVRAHESVVKSEDFSLPAYMDRRDHPLPEVAHVKHLSASQKALKEKEKASWSSLSMDEKVELYRIKFKESFAEMNRGSNEWKTVVGGAMFFIGFTALVIMWQKHYVYGPLPQSFDKEWVAKQTKRMLDMKVNPIQGLASKWDYEKNEWKK/
+    MLGAALRRCAVAATTRADPRGLLHSARTPGPAVAIQSVRCYSHGSQETDEEFDARWVTYFNKPDIDAWELRKGINTLVTYDMVPEPKIIDAALRACRRLNDFASTVRILEVVKDKAGPHKEIYPYVIQELRPTLNELGISTPEELGLDKV/
+    MASRLLRGAGTLAAQALRARGPSGAAAMRSMASGGGVPTDEEQATGLEREIMLAAKKGLDPYNVLAPKGASGTREDPNLVPSISNKRIVGCICEEDNTSVVWFWLHKGEAQRCPRCGAHYKLVPQQLAH/
+    MALPLRPLTRGLASAAKGGHGGAGARTWRLLTFVLALPSVALCTFNSYLHSGHRPRPEFRPYQHLRIRTKPYPWGDGNHTLFHNSHVNPLPTGYEHP/
+    MAEDMETKIKNYKTAPFDSRFPNQNQTRNCWQNYLDFHRCQKAMTAKGGDISVCEWYQRVYQSLCPTSWVTDWDEQRAEGTFPGKI/
+    MAPEVLPKPRMRGLLARRLRNHMAVAFVLSLGVAALYKFRVADQRKKAYADFYRNYDVMKDFEEMRKAGIFQSVK/
+    MQALRVSQALIRSFSSTARNRFQNRVREKQKLFQEDNDIPLYLKGGIVDNILYRVTMTLCLGGTVYSLYSLGWASFPRN/
+    MFPLVKSALNRLQVRSIQQTMARQSHQKRTPDFHDKYGNAVLASGATFCIVTWTYVATQVGIEWNLSPVGRVTPKEWRNQ/
+    MLGQSIRRFTTSVVRRSHYEEGPGKNLPFSVENKWSLLAKMCLYFGSAFATPFLVVRHQLLKT/
+    MSVLTPLLLRGLTGSARRLPVPRAKIHSLPPEGKLGIMELAVGLTSCFVTFLLPAGWILSHLETYRRPE/
+    MFADRWLFSTNHKDIGTLYLLFGAWAGVLGTALSLLIRAELGQPGNLLGNDHIYNVIVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSLLLLLASAMVEAGAGTGWTVYPPLAGNYSHPGASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAMTQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIVTYYSGKKEPFGYMGMVWAMMSIGFLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAIPTGVKVFSWLATLHGSNMKWSAAVLWALGFIFLFTVGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFIHWFPLFSGYTLDQTYAKIHFTIMFIGVNLTFFPQHFLGLSGMPRRYSDYPDAYTTWNILSSVGSFISLTAVMLMIFMIWEAFASKRKVLMVEEPSMNLEWLYGCPPPYHTFEEPVYMK-S/
+    MAHAAQVGLQDATSPIMEELITFHDHALMIIFLICFLVLYALFLTLTTKLTNTNISDAQEMETVWTILPAIILVLIALPSLRILYMTDEVNDPSLTIKSIGHQWYWTYEYTDYGGLIFNSYMLPPLFLEPGDLRLLDVDNRVVLPIEAPIRMMITSQDVLHSWAVPTLGLKTDAIPGRLNQTTFTATRPGVYYGQCSEICGANHSFMPIVLELIPLKIFEMGPVFTL/
+    MTHQSHAYHMVKPSPWPLTGALSALLMTSGLAMWFHFHSMTLLMLGLLTNTLTMYQWWRDVTRESTYQGHHTPPVQKGLRYGMILFITSEVFFFAGFFWAFYHSSLAPTPQLGGHWPPTGITPLNPLEVPLLNTSVLLASGVSITWAHHSLMENNRNQMIQALLITILLGLYFTLLQASEYFESPFTISDGIYGSTFFVATGFHGLHVIIGSTFLTICFIRQLMFHFTSKHHFGFEAAAWYWHFVDVVWLFLYVSIYWWGS/
+    MLATRVFSLVGKRAISTSVCVRAHESVVKSEDFSLPAYMDRRDHPLPEVAHVKHLSASQKALKEKEKASWSSLSMDEKVELYRIKFKESFAEMNRGSNEWKTVVGGAMFFIGFTALVIMWQKHYVYGPLPQSFDKEWVAKQTKRMLDMKVNPIQGLASKWDYEKNEWKK/
+    MLGAALRRCAVAATTRADPRGLLHSARTPGPAVAIQSVRCYSHGSQETDEEFDARWVTYFNKPDIDAWELRKGINTLVTYDMVPEPKIIDAALRACRRLNDFASTVRILEVVKDKAGPHKEIYPYVIQELRPTLNELGISTPEELGLDKV/
+    MASRLLRGAGTLAAQALRARGPSGAAAMRSMASGGGVPTDEEQATGLEREIMLAAKKGLDPYNVLAPKGASGTREDPNLVPSISNKRIVGCICEEDNTSVVWFWLHKGEAQRCPRCGAHYKLVPQQLAH/
+    MALPLRPLTRGLASAAKGGHGGAGARTWRLLTFVLALPSVALCTFNSYLHSGHRPRPEFRPYQHLRIRTKPYPWGDGNHTLFHNSHVNPLPTGYEHP/
+    MAEDMETKIKNYKTAPFDSRFPNQNQTRNCWQNYLDFHRCQKAMTAKGGDISVCEWYQRVYQSLCPTSWVTDWDEQRAEGTFPGKI/
+    MAPEVLPKPRMRGLLARRLRNHMAVAFVLSLGVAALYKFRVADQRKKAYADFYRNYDVMKDFEEMRKAGIFQSVK/
+    MQALRVSQALIRSFSSTARNRFQNRVREKQKLFQEDNDIPLYLKGGIVDNILYRVTMTLCLGGTVYSLYSLGWASFPRN/
+    MFPLVKSALNRLQVRSIQQTMARQSHQKRTPDFHDKYGNAVLASGATFCIVTWTYVATQVGIEWNLSPVGRVTPKEWRNQ/
+    MLGQSIRRFTTSVVRRSHYEEGPGKNLPFSVENKWSLLAKMCLYFGSAFATPFLVVRHQLLKT/
+    MSVLTPLLLRGLTGSARRLPVPRAKIHSLPPEGKLGIMELAVGLTSCFVTFLLPAGWILSHLETYRRPE*
+
+
+
+```python
+a = modeller.automodel.automodel(env, alnfile='big_one.ali', knowns= ('1v55'), sequence = '9606' )
+a.name='mod9606'
+a.starting_model = 1
+a.ending_model = 1
+a.make()
+
+
+```
+
+    
+    check_ali___> Checking the sequence-structure alignment. 
+    
+    Implied target CA(i)-CA(i+1) distances longer than  8.0 angstroms:
+    
+    ALN_POS  TMPL  RID1  RID2  NAM1  NAM2     DIST
+    ----------------------------------------------
+    END OF TABLE
+    read_to_681_> topology.submodel read from topology file:        3
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16   513
+                  atom names           : C     +N
+                  atom indices         :  4027     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16   513
+                  atom names           : C     CA    +N    O
+                  atom indices         :  4027  4024     0  4028
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    10   740
+                  atom names           : C     +N
+                  atom indices         :  5825     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    10   740
+                  atom names           : C     CA    +N    O
+                  atom indices         :  5825  5820     0  5826
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16  1001
+                  atom names           : C     +N
+                  atom indices         :  7952     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16  1001
+                  atom names           : C     CA    +N    O
+                  atom indices         :  7952  7949     0  7953
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:     9  1170
+                  atom names           : C     +N
+                  atom indices         :  9330     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:     9  1170
+                  atom names           : C     CA    +N    O
+                  atom indices         :  9330  9324     0  9331
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    18  1320
+                  atom names           : C     +N
+                  atom indices         : 10509     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    18  1320
+                  atom names           : C     CA    +N    O
+                  atom indices         : 10509 10505     0 10510
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:     7  1449
+                  atom names           : C     +N
+                  atom indices         : 11466     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:     7  1449
+                  atom names           : C     CA    +N    O
+                  atom indices         : 11466 11459     0 11467
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    13  1546
+                  atom names           : C     +N
+                  atom indices         : 12234     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    13  1546
+                  atom names           : C     CA    +N    O
+                  atom indices         : 12234 12230     0 12235
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:     8  1632
+                  atom names           : C     +N
+                  atom indices         : 12949     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:     8  1632
+                  atom names           : C     CA    +N    O
+                  atom indices         : 12949 12944     0 12950
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:     9  1707
+                  atom names           : C     +N
+                  atom indices         : 13566     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:     9  1707
+                  atom names           : C     CA    +N    O
+                  atom indices         : 13566 13560     0 13567
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    12  1786
+                  atom names           : C     +N
+                  atom indices         : 14208     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    12  1786
+                  atom names           : C     CA    +N    O
+                  atom indices         : 14208 14203     0 14209
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    14  1866
+                  atom names           : C     +N
+                  atom indices         : 14854     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    14  1866
+                  atom names           : C     CA    +N    O
+                  atom indices         : 14854 14848     0 14855
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    17  1929
+                  atom names           : C     +N
+                  atom indices         : 15365     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    17  1929
+                  atom names           : C     CA    +N    O
+                  atom indices         : 15365 15361     0 15366
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:     4  1998
+                  atom names           : C     +N
+                  atom indices         : 15898     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:     4  1998
+                  atom names           : C     CA    +N    O
+                  atom indices         : 15898 15892     0 15899
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16  2511
+                  atom names           : C     +N
+                  atom indices         : 19927     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16  2511
+                  atom names           : C     CA    +N    O
+                  atom indices         : 19927 19924     0 19928
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    10  2738
+                  atom names           : C     +N
+                  atom indices         : 21725     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    10  2738
+                  atom names           : C     CA    +N    O
+                  atom indices         : 21725 21720     0 21726
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16  2999
+                  atom names           : C     +N
+                  atom indices         : 23852     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    16  2999
+                  atom names           : C     CA    +N    O
+                  atom indices         : 23852 23849     0 23853
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:     9  3168
+                  atom names           : C     +N
+                  atom indices         : 25230     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:     9  3168
+                  atom names           : C     CA    +N    O
+                  atom indices         : 25230 25224     0 25231
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    18  3318
+                  atom names           : C     +N
+                  atom indices         : 26409     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    18  3318
+                  atom names           : C     CA    +N    O
+                  atom indices         : 26409 26405     0 26410
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:     7  3447
+                  atom names           : C     +N
+                  atom indices         : 27366     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:     7  3447
+                  atom names           : C     CA    +N    O
+                  atom indices         : 27366 27359     0 27367
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    13  3544
+                  atom names           : C     +N
+                  atom indices         : 28134     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    13  3544
+                  atom names           : C     CA    +N    O
+                  atom indices         : 28134 28130     0 28135
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:     8  3630
+                  atom names           : C     +N
+                  atom indices         : 28849     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:     8  3630
+                  atom names           : C     CA    +N    O
+                  atom indices         : 28849 28844     0 28850
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:     9  3705
+                  atom names           : C     +N
+                  atom indices         : 29466     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:     9  3705
+                  atom names           : C     CA    +N    O
+                  atom indices         : 29466 29460     0 29467
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    12  3784
+                  atom names           : C     +N
+                  atom indices         : 30108     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    12  3784
+                  atom names           : C     CA    +N    O
+                  atom indices         : 30108 30103     0 30109
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    14  3864
+                  atom names           : C     +N
+                  atom indices         : 30754     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    14  3864
+                  atom names           : C     CA    +N    O
+                  atom indices         : 30754 30748     0 30755
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    17  3927
+                  atom names           : C     +N
+                  atom indices         : 31265     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:    17  3927
+                  atom names           : C     CA    +N    O
+                  atom indices         : 31265 31261     0 31266
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:     4  3996
+                  atom names           : C     +N
+                  atom indices         : 31798     0
+    
+    getf_______W> RTF restraint not found in the atoms list:
+                  residue type, indices:     4  3996
+                  atom names           : C     CA    +N    O
+                  atom indices         : 31798 31792     0 31799
+    The following 28 residues contain 6-membered rings with poor geometries
+    after transfer from templates. Rebuilding rings from internal coordinates:
+       <Residue 377:A (type PHE)>
+       <Residue 502:A (type TYR)>
+       <Residue 536:B (type PHE)>
+       <Residue 618:B (type TYR)>
+       <Residue 748:C (type TYR)>
+       <Residue 775:C (type PHE)>
+       <Residue 842:C (type TYR)>
+       <Residue 943:C (type PHE)>
+       <Residue 965:C (type PHE)>
+       <Residue 1423:F (type PHE)>
+       <Residue 1511:G (type TYR)>
+       <Residue 1531:G (type PHE)>
+       <Residue 1583:H (type PHE)>
+       <Residue 1819:K (type PHE)>
+       <Residue 2375:N (type PHE)>
+       <Residue 2500:N (type TYR)>
+       <Residue 2534:O (type PHE)>
+       <Residue 2616:O (type TYR)>
+       <Residue 2746:P (type TYR)>
+       <Residue 2773:P (type PHE)>
+       <Residue 2836:P (type PHE)>
+       <Residue 2840:P (type TYR)>
+       <Residue 2941:P (type PHE)>
+       <Residue 2963:P (type PHE)>
+       <Residue 3509:T (type TYR)>
+       <Residue 3529:T (type PHE)>
+       <Residue 3581:U (type PHE)>
+       <Residue 3817:X (type PHE)>
+    mdtrsr__446W> A potential that relies on one protein is used, yet you have at
+                  least one known structure available. MDT, not library, potential is used.
+    0 atoms in HETATM/BLK residues constrained
+    to protein atoms within 2.30 angstroms
+    and protein CA atoms within 10.00 angstroms
+    0 atoms in residues without defined topology
+    constrained to be rigid bodies
+    condens_443_> Restraints marked for deletion were removed.
+                  Total number of restraints before, now:   351583   322941
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_484W> Dihedral still outside +-90:      -90.3017
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_484W> Dihedral still outside +-90:       90.0671
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
+    
+    
+    >> ENERGY; Differences between the model's features and restraints:
+    Number of all residues in MODEL                   :     3996
+    Number of all, selected real atoms                :    31800   31800
+    Number of all, selected pseudo atoms              :        0       0
+    Number of all static, selected restraints         :   322941  322941
+    COVALENT_CYS                                      :        F
+    NONBONDED_SEL_ATOMS                               :        1
+    Number of non-bonded pairs (excluding 1-2,1-3,1-4):    79302
+    Dynamic pairs routine                             : 2, NATM x NATM cell sorting
+    Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
+    LENNARD_JONES_SWITCH                              :    6.500   7.500
+    COULOMB_JONES_SWITCH                              :    6.500   7.500
+    RESIDUE_SPAN_RANGE                                :        0   99999
+    NLOGN_USE                                         :       15
+    CONTACT_SHELL                                     :    4.000
+    DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
+    SPHERE_STDV                                       :    0.050
+    RADII_FACTOR                                      :    0.820
+    Current energy                                    :       20600.9121
+    
+    
+    
+    
+    
+    Summary of the restraint violations: 
+    
+       NUM     ... number of restraints.
+       NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
+       RVIOL   ... relative difference from the best value.
+       NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
+       RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
+       RMS_2   ... RMS(feature, best_value, NUMB).
+       MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
+    
+     #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
+    ------------------------------------------------------------------------------------------------------
+     1 Bond length potential              :   32732       0      0   0.005   0.005      211.11       1.000
+     2 Bond angle potential               :   44520       6     85   2.036   2.036      3523.7       1.000
+     3 Stereochemical cosine torsion poten:   22664       0    540  44.600  44.600      6718.7       1.000
+     4 Stereochemical improper torsion pot:   14014       0      5   1.313   1.313      488.93       1.000
+     5 Soft-sphere overlap restraints     :   79302       0      4   0.004   0.004      165.31       1.000
+     6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
+     7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
+     8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
+     9 Distance restraints 1 (CA-CA)      :   85829       0     22   0.234   0.234      1590.4       1.000
+    10 Distance restraints 2 (N-O)        :   82391       7    149   0.319   0.319      2980.2       1.000
+    11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
+    12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
+    13 Mainchain Omega dihedral restraints:    3970      10     38   8.050   8.050      781.51       1.000
+    14 Sidechain Chi_1 dihedral restraints:    3402       0     52  82.119  82.119      1156.3       1.000
+    15 Sidechain Chi_2 dihedral restraints:    2578       0     25  82.115  82.115      1012.2       1.000
+    16 Sidechain Chi_3 dihedral restraints:    1030       0      1  76.972  76.972      624.68       1.000
+    17 Sidechain Chi_4 dihedral restraints:     352       0      0  94.889  94.889      238.14       1.000
+    18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
+    19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
+    20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
+    21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    23 Distance restraints 3 (SDCH-MNCH)  :   23111       0      0   0.297   0.297      236.76       1.000
+    24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
+    25 Phi/Psi pair of dihedral restraints:    3944     663    375  26.961  72.073      690.46       1.000
+    26 Distance restraints 4 (SDCH-SDCH)  :    2404       0      2   0.912   0.912      182.64       1.000
+    27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
+    28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
+    29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
+    30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
+    31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
+    32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
+    33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
+    34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
+    35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
+    36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
+    37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
+    38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
+    39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000
+    
+    
+    
+    # Heavy relative violation of each residue is written to: 9606.V99990001
+    # The profile is NOT normalized by the number of restraints.
+    # The profiles are smoothed over a window of residues:    1
+    # The sum of all numbers in the file:  452454.7812
+    
+    
+    
+    List of the violated restraints:
+       A restraint is violated when the relative difference
+       from the best value (RVIOL) is larger than CUTOFF.
+    
+       ICSR   ... index of a restraint in the current set.
+       RESNO  ... residue numbers of the first two atoms.
+       ATM    ... IUPAC atom names of the first two atoms.
+       FEAT   ... the value of the feature in the model.
+       restr  ... the mean of the basis restraint with the smallest
+                  difference from the model (local minimum).
+       viol   ... difference from the local minimum.
+       rviol  ... relative difference from the local minimum.
+       RESTR  ... the best value (global minimum).
+       VIOL   ... difference from the best value.
+       RVIOL  ... relative difference from the best value.
+    
+    
+    -------------------------------------------------------------------------------------------------
+    
+    Feature  2                           : Bond angle potential                    
+    List of the RVIOL violations larger than   :       4.5000
+    
+        #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
+        1  40535 702P 702P N   CA   5526 5527  136.20  108.20   28.00    6.36  108.20   28.00    6.36
+        2  43883 994V 994V N   CA   7883 7884  122.88  107.00   15.88    4.57  107.00   15.88    4.57
+        3  442111024A1024A N   CA   8120 8121  122.76  107.00   15.76    4.53  107.00   15.76    4.53
+        4  488911455R1455R N   CA  1150511506  124.85  107.00   17.85    5.13  107.00   17.85    5.13
+        5  554642042P2042P N   CA  1623816239  130.79  108.20   22.59    5.13  108.20   22.59    5.13
+        6  627952700P2700P N   CA  2142621427  137.07  108.20   28.87    6.56  108.20   28.87    6.56
+    
+    -------------------------------------------------------------------------------------------------
+    
+    Feature 10                           : Distance restraints 2 (N-O)             
+    List of the RVIOL violations larger than   :       4.5000
+    
+        #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
+        1 215163   8F 753P N   O      66 5935    7.47    5.01    2.46    4.58    5.01    2.46    4.58
+        2 233054 668T 613I N   O    5266 4811    7.01    4.69    2.33    4.64    4.69    2.33    4.64
+        3 233078 669S 613I N   O    5273 4811    6.13    3.04    3.09    6.31    3.04    3.09    6.31
+        4 236370 793T 789T N   O    6234 6210    5.42    3.00    2.41    4.60    3.00    2.41    4.60
+        5 241249 996I 992L N   O    7896 7870    5.88    3.39    2.49    4.79    3.39    2.49    4.79
+        6 2867113273T3307I N   O   2604526328    8.29    5.60    2.69    4.57    5.60    2.69    4.57
+        7 2932583671V3666L N   O   2917029126    5.54    3.19    2.35    4.90    3.19    2.35    4.90
+    
+    -------------------------------------------------------------------------------------------------
+    
+    Feature 13                           : Mainchain Omega dihedral restraints     
+    List of the RVIOL violations larger than   :       4.5000
+    
+        #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
+        1 118371 497G 497G CA  C    3892 3893   -2.33 -179.18  176.85   41.10 -179.18  176.85   41.10
+        2 118574 701R 701R CA  C    5516 5524 -145.15 -180.00   34.85    6.97 -180.00   34.85    6.97
+        3 118727 855H 855H CA  C    6754 6761    0.35 -179.18  179.53   41.73 -179.18  179.53   41.73
+        4 1199022041Q2041Q CA  C   1623016236 -147.91 -180.00   32.09    6.42 -180.00   32.09    6.42
+        5 1203562495G2495G CA  C   1979219793   -1.32 -179.18  177.86   41.34 -179.18  177.86   41.34
+        6 1205592699R2699R CA  C   2141621424 -142.55 -180.00   37.45    7.49 -180.00   37.45    7.49
+        7 1207122853H2853H CA  C   2265422661    0.47 -179.18  179.66   41.75 -179.18  179.66   41.75
+        8 1212183362A3362A CA  C   2670526707 -156.37 -180.00   23.63    4.72 -180.00   23.63    4.72
+        9 1217763926K3926K CA  C   3125231258   -0.22 -179.18  178.97   41.59 -179.18  178.97   41.59
+    
+    -------------------------------------------------------------------------------------------------
+    
+    Feature 25                           : Phi/Psi pair of dihedral restraints     
+    List of the RVIOL violations larger than   :       6.5000
+    
+        #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
+        1 113945  15I  16G C   N     131  133  -62.60  -62.40    0.61    0.10   82.20  153.28   11.66
+        1         16G  16G N   CA    133  134  -41.78  -41.20                    8.50
+        2 113956  26A  27G C   N     217  219  -63.79  -62.40    2.18    0.40   82.20  154.77   11.79
+        2         27G  27G N   CA    219  220  -42.88  -41.20                    8.50
+        3 113959  29L  30G C   N     236  238  -64.71  -62.40    3.51    0.64   82.20  155.96   11.89
+        3         30G  30G N   CA    238  239  -43.84  -41.20                    8.50
+        4 113971  41L  42G C   N     323  325 -136.24 -167.20   31.11    0.53   82.20 -144.10   16.31
+        4         42G  42G N   CA    325  326  171.52  174.60                    8.50
+        5 113972  42G  43Q C   N     327  329  -64.84  -63.80    9.63    1.36 -121.10  179.48    7.44
+        5         43Q  43Q N   CA    329  330  -30.73  -40.30                  139.70
+        6 113977  47L  48L C   N     363  365   67.29   60.20   13.57    0.50  -63.50  143.58   26.45
+        6         48L  48L N   CA    365  366   18.03   29.60                  -41.20
+        7 114005  75I  76G C   N     588  590  -71.63  -62.40   24.70    4.18   82.20  170.11   13.18
+        7         76G  76G N   CA    590  591  -64.11  -41.20                    8.50
+        8 114006  76G  77G C   N     592  594  -67.91  -62.40    5.53    0.96   82.20  157.95   11.97
+        8         77G  77G N   CA    594  595  -40.65  -41.20                    8.50
+        9 114008  78F  79G C   N     607  609  -64.93  -62.40    2.53    0.46   82.20  155.33   11.80
+        9         79G  79G N   CA    609  610  -41.29  -41.20                    8.50
+       10 114016  86M  87I C   N     671  673   64.04  -63.40  167.38   31.52 -120.60 -172.85   14.60
+       10         87I  87I N   CA    673  674   64.91  -43.60                  130.30
+       11 114020  90P  91D C   N     695  697  -83.35  -70.90   20.57    0.73  -63.30  154.64   20.35
+       11         91D  91D N   CA    697  698  166.67  150.30                  -40.00
+       12 114047 117M 118V C   N     908  910   44.32  -73.50  138.52   11.31 -125.40 -176.89    9.17
+       12        118V 118V N   CA    910  911 -147.95  139.20                  143.30
+       13 114049 119E 120A C   N     924  926  102.89 -134.00  127.12    3.17  -62.50 -143.04   34.18
+       13        120A 120A N   CA    926  927  178.68  147.00                  -40.90
+       14 114052 122A 123G C   N     938  940 -136.76  -62.40   80.52   12.83   82.20  142.28    8.80
+       14        123G 123G N   CA    940  941  -10.31  -41.20                    8.50
+       15 114053 123G 124T C   N     942  944   94.68   55.90  128.34   11.90 -124.80  141.71    7.02
+       15        124T 124T N   CA    944  945  161.83   39.50                  143.50
+       16 114056 126W 127T C   N     967  969   55.89   55.90    7.30    0.51  -63.20  148.61   25.56
+       16        127T 127T N   CA    969  970   46.80   39.50                  -42.10
+       17 114067 137S 138H C   N    1050 1052  -63.79  -63.20   12.37    1.58 -125.60  177.64    7.72
+       17        138H 138H N   CA   1052 1053  -54.66  -42.30                  138.80
+       18 114083 153A 154G C   N    1168 1170  -63.27  -62.40    2.55    0.43   82.20  154.52   11.78
+       18        154G 154G N   CA   1170 1171  -43.60  -41.20                    8.50
+       19 114099 169I 170N C   N    1281 1283 -111.13 -119.90   86.86    3.74  -63.20  103.46   11.14
+       19        170N 170N N   CA   1283 1284   50.59  137.00                  -41.10
+       20 114144 214N 215L C   N    1627 1629   73.53   60.20   15.77    1.14  -63.50  150.56   27.73
+       20        215L 215L N   CA   1629 1630   21.18   29.60                  -41.20
+       21 114146 216N 217T C   N    1643 1645 -142.27 -124.80   81.56    4.01  -63.20  132.19   14.03
+       21        217T 217T N   CA   1645 1646   63.83  143.50                  -42.10
+       22 114179 249P 250G C   N    1916 1918  -64.26  -62.40    4.61    0.63   82.20  153.36   11.58
+       22        250G 250G N   CA   1918 1919  -36.98  -41.20                    8.50
+       23 114181 251F 252G C   N    1931 1933  -66.85  -62.40    5.91    0.85   82.20  155.94   11.77
+       23        252G 252G N   CA   1933 1934  -37.31  -41.20                    8.50
+       24 114190 260Y 261Y C   N    2001 2003  -82.29  -63.50   67.20    9.78  -63.50   67.20    9.78
+       24        261Y 261Y N   CA   2003 2004   21.12  -43.40                  -43.40
+       25 114191 261Y 262S C   N    2013 2015   56.91   56.90    2.03    0.13  -64.10  141.56   18.59
+       25        262S 262S N   CA   2015 2016   38.43   36.40                  -35.00
+       26 114196 266E 267P C   N    2050 2052  -66.29  -58.70   20.64    1.23  -64.50  158.52   11.92
+       26        267P 267P N   CA   2052 2053  -11.31  -30.50                  147.20
+       27 114197 267P 268F C   N    2057 2059 -177.23 -124.20   79.45    4.39  -63.20  171.75   19.58
+       27        268F 268F N   CA   2059 2060   84.14  143.30                  -44.30
+       28 114198 268F 269G C   N    2068 2070  -66.11  -62.40    6.69    1.19   82.20  158.27   12.10
+       28        269G 269G N   CA   2070 2071  -46.77  -41.20                    8.50
+       29 114201 271M 272G C   N    2092 2094  -62.21  -62.40    0.49    0.07   82.20  152.88   11.63
+       29        272G 272G N   CA   2094 2095  -41.66  -41.20                    8.50
+       30 114214 284G 285F C   N    2187 2189 -119.31 -124.20   90.54    4.15  -63.20  112.23   12.74
+       30        285F 285F N   CA   2189 2190   52.89  143.30                  -44.30
+       31 114215 285F 286I C   N    2198 2200 -136.87  -63.40  101.81   15.69  -63.40  101.81   15.69
+       31        286I 286I N   CA   2200 2201   26.88  -43.60                  -43.60
+       32 114220 290H 291H C   N    2242 2244 -122.55 -125.60   79.06    2.95  -63.20  118.10   12.56
+       32        291H 291H N   CA   2244 2245   59.80  138.80                  -42.30
+       33 114223 293F 294T C   N    2271 2273  -85.23  -63.20   93.94   10.74  -63.20   93.94   10.74
+       33        294T 294T N   CA   2273 2274   49.22  -42.10                  -42.10
+       34 114226 296G 297M C   N    2289 2291  -68.99  -73.00   14.41    1.05  -63.40  162.75   24.74
+       34        297M 297M N   CA   2291 2292  156.84  143.00                  -40.50
+       35 114246 316T 317G C   N    2442 2444  -60.21  -62.40    2.34    0.44   82.20  150.57   11.45
+       35        317G 317G N   CA   2444 2445  -40.39  -41.20                    8.50
+       36 114262 332M 333K C   N    2564 2566 -113.15 -118.00   56.37    2.67  -62.90  133.55   15.43
+       36        333K 333K N   CA   2566 2567   82.94  139.10                  -40.80
+       37 114272 342L 343G C   N    2645 2647  -61.35  -62.40    3.44    0.47   82.20  153.01   11.69
+       37        343G 343G N   CA   2647 2648  -44.47  -41.20                    8.50
+       38 114280 350V 351G C   N    2712 2714  -59.04  -62.40    4.29    0.80   82.20  148.87   11.30
+       38        351G 351G N   CA   2714 2715  -38.53  -41.20                    8.50
+       39 114320 390M 391G C   N    3014 3016  -65.60  -62.40    3.43    0.55   82.20  155.55   11.79
+       39        391G 391G N   CA   3016 3017  -39.96  -41.20                    8.50
+       40 114330 400F 401S C   N    3102 3104   79.37   56.90   33.76    1.86  -64.10  150.73   20.16
+       40        401S 401S N   CA   3104 3105   11.21   36.40                  -35.00
+       41 114331 401S 402G C   N    3108 3110 -119.42  -80.20   40.60    2.94   82.20 -138.32   17.03
+       41        402G 402G N   CA   3110 3111  163.62  174.10                    8.50
+       42 114363 433L 434S C   N    3373 3375   83.52   56.90   27.51    2.83  -64.10  161.07   21.49
+       42        434S 434S N   CA   3375 3376   29.45   36.40                  -35.00
+       43 114364 434S 435G C   N    3379 3381  -73.10  -80.20   39.58    1.22   82.20 -159.60    7.07
+       43        435G 435G N   CA   3381 3382  135.16  174.10                    8.50
+       44 114367 437P 438R C   N    3398 3400   63.57   57.30   10.59    0.58 -125.20 -155.86   10.76
+       44        438R 438R N   CA   3400 3401   29.46   38.00                  140.60
+       45 114386 456V 457G C   N    3561 3563  -58.68  -62.40    8.50    1.47   82.20  147.03   11.07
+       45        457G 457G N   CA   3563 3564  -33.56  -41.20                    8.50
+       46 114407 477A 478S C   N    3726 3728   56.53   56.90   21.24    1.32  -64.10  152.10   19.50
+       46        478S 478S N   CA   3728 3729   57.64   36.40                  -35.00
+       47 114411 481K 482V C   N    3761 3763 -121.03  -62.40   64.03   10.92  -62.40   64.03   10.92
+       47        482V 482V N   CA   3763 3764  -68.14  -42.40                  -42.40
+       48 114415 485V 486E C   N    3791 3793   60.97   54.60    8.29    0.56  -63.60  146.66   25.24
+       48        486E 486E N   CA   3793 3794   37.10   42.40                  -40.30
+       49 114424 494W 495L C   N    3869 3871  -99.68 -108.50   75.77    4.00  -63.50  104.88   13.01
+       49        495L 495L N   CA   3871 3872   57.24  132.50                  -41.20
+       50 114425 495L 496Y C   N    3877 3879   65.83   55.90  115.65    8.84 -124.30  170.96   12.22
+       50        496Y 496Y N   CA   3879 3880  154.72   39.50                  135.40
+       51 114426 496Y 497G C   N    3889 3891 -118.57  -80.20   64.52    4.31   82.20 -164.33   15.28
+       51        497G 497G N   CA   3891 3892  122.23  174.10                    8.50
+       52 114433 503H 504T C   N    3942 3944   53.51   55.90    7.69    0.39  -63.20  146.72   25.23
+       52        504T 504T N   CA   3944 3945   46.81   39.50                  -42.10
+       53 114440 510Y 511M C   N    4004 4006  -85.11  -73.00   21.37    1.33  -63.40  160.37   25.67
+       53        511M 511M N   CA   4006 4007  160.61  143.00                  -40.50
+       54 114441 511M 512K C   N    4012 4014  -70.92  -70.20    0.72    0.05  -62.90  178.94   23.68
+       54        512K 512K N   CA   4014 4015  140.44  140.40                  -40.80
+       55 114444 516H 517A C   N    4051 4053   55.73   55.40    3.74    0.25  -62.50  144.35   29.28
+       55        517A 517A N   CA   4053 4054   41.92   38.20                  -40.90
+       56 114497 569S 570D C   N    4465 4467 -133.92  -96.50   80.68    3.34  -63.30  108.77   11.95
+       56        570D 570D N   CA   4467 4468   42.72  114.20                  -40.00
+       57 114499 571A 572Q C   N    4478 4480 -165.82  -63.80  104.87   18.44  -63.80  104.87   18.44
+       57        572Q 572Q N   CA   4480 4481  -64.58  -40.30                  -40.30
+       58 114530 602E 603V C   N    4728 4730 -130.10 -125.40   11.79    0.67  -62.40 -172.47   20.79
+       58        603V 603V N   CA   4730 4731  132.49  143.30                  -42.40
+       59 114531 603V 604N C   N    4735 4737  -87.96  -71.20   25.86    2.06   55.90  166.39   13.06
+       59        604N 604N N   CA   4737 4738  123.11  142.80                   39.50
+       60 114540 612S 613I C   N    4802 4804  -63.66  -63.40    3.54    0.59 -120.60 -173.65    8.58
+       60        613I 613I N   CA   4804 4805  -47.14  -43.60                  130.30
+       61 114543 615H 616Q C   N    4824 4826   73.50   55.10   26.15    1.63 -121.10 -156.84   10.04
+       61        616Q 616Q N   CA   4826 4827   21.73   40.30                  139.70
+       62 114550 622E 623Y C   N    4901 4903 -117.86  -98.40   87.67    9.03  -63.50  102.01   14.12
+       62        623Y 623Y N   CA   4903 4904   42.92  128.40                  -43.40
+       63 114552 624T 625D C   N    4920 4922 -122.45  -63.30   60.22   10.00  -63.30   60.22   10.00
+       63        625D 625D N   CA   4922 4923  -51.32  -40.00                  -40.00
+       64 114554 626Y 627G C   N    4940 4942  -91.36  -80.20   76.23    3.56   82.20 -164.40    8.84
+       64        627G 627G N   CA   4942 4943   98.69  174.10                    8.50
+       65 114569 641L 642E C   N    5058 5060  -55.29  -63.60   24.14    2.85  -69.30  155.17   12.32
+       65        642E 642E N   CA   5060 5061  -62.96  -40.30                  142.50
+       66 114570 642E 643P C   N    5067 5069  -73.13  -58.70   25.53    1.55  -64.50  156.87   12.17
+       66        643P 643P N   CA   5069 5070   -9.44  -30.50                  147.20
+       67 114586 658P 659I C   N    5192 5194   -5.91  -97.30   98.73    5.77  -63.40  145.28   25.92
+       67        659I 659I N   CA   5194 5195   89.83  127.20                  -43.60
+       68 114597 669S 670Q C   N    5277 5279 -128.97  -63.80   92.15   16.58  -63.80   92.15   16.58
+       68        670Q 670Q N   CA   5279 5280 -105.44  -40.30                  -40.30
+       69 114598 670Q 671D C   N    5286 5288  -81.58  -70.90   40.23    1.51  -63.30  132.19   17.47
+       69        671D 671D N   CA   5288 5289 -170.92  150.30                  -40.00
+       70 114608 680T 681L C   N    5365 5367   68.94   60.20   12.17    1.40  -63.50  154.35   28.45
+       70        681L 681L N   CA   5367 5368   38.06   29.60                  -41.20
+       71 114615 687A 688I C   N    5414 5416  -63.90  -63.40   10.29    1.67 -120.60  173.17    7.86
+       71        688I 688I N   CA   5416 5417  -33.33  -43.60                  130.30
+       72 114616 688I 689P C   N    5422 5424  -95.36  -58.70   45.17    3.73  -64.50  154.43   13.20
+       72        689P 689P N   CA   5424 5425   -4.11  -30.50                  147.20
+       73 114617 689P 690G C   N    5429 5431 -129.54 -167.20   38.21    0.60   82.20 -142.13   16.59
+       73        690G 690G N   CA   5431 5432  168.15  174.60                    8.50
+       74 114629 701R 702P C   N    5524 5526  -21.23  -58.70   70.58    4.19  -64.50  129.90   12.03
+       74        702P 702P N   CA   5526 5527  -90.32  -30.50                  147.20
+       75 114634 706Y 707G C   N    5566 5568 -142.38 -167.20   26.08    0.38   82.20 -151.86   15.70
+       75        707G 707G N   CA   5568 5569  166.58  174.60                    8.50
+       76 114663 735G 736P C   N    5785 5787  -67.78  -64.50   22.66    1.53  -58.70  160.14   13.98
+       76        736P 736P N   CA   5787 5788  169.62  147.20                  -30.50
+       77 114664 736P 737V C   N    5792 5794   38.42  -62.40  129.13   21.89  -62.40  129.13   21.89
+       77        737V 737V N   CA   5794 5795   38.29  -42.40                  -42.40
+       78 114665 737V 738F C   N    5799 5801 -135.12  -63.20   88.25   10.79  -63.20   88.25   10.79
+       78        738F 738F N   CA   5801 5802    6.84  -44.30                  -44.30
+       79 114666 738F 739T C   N    5810 5812  -64.03  -63.20    0.93    0.12 -124.80 -174.93    9.68
+       79        739T 739T N   CA   5812 5813  -41.69  -42.10                  143.50
+       80 114669 743H 744Q C   N    5851 5853 -114.62  -63.80   96.39   12.36  -63.80   96.39   12.36
+       80        744Q 744Q N   CA   5853 5854   41.60  -40.30                  -40.30
+       81 114671 745S 746H C   N    5866 5868 -109.20  -63.20   85.82    9.15  -63.20   85.82    9.15
+       81        746H 746H N   CA   5868 5869   30.15  -42.30                  -42.30
+       82 114675 749H 750M C   N    5903 5905  -87.93  -73.00   16.72    1.13  -63.40  170.75   27.45
+       82        750M 750M N   CA   5905 5906  150.52  143.00                  -40.50
+       83 114678 752K 753P C   N    5927 5929  -66.71  -58.70   42.19    4.15  -64.50  140.90   10.40
+       83        753P 753P N   CA   5929 5930  -71.92  -30.50                  147.20
+       84 114679 753P 754S C   N    5934 5936   83.77   56.90   71.60    2.93  -64.10  147.96   19.13
+       84        754S 754S N   CA   5936 5937  -29.96   36.40                  -35.00
+       85 114702 776H 777F C   N    6108 6110   62.26   58.10    5.20    0.79  -63.20  148.96   26.87
+       85        777F 777F N   CA   6110 6111   36.01   32.90                  -44.30
+       86 114714 788L 789T C   N    6202 6204  -69.46  -78.10   19.47    1.12  -63.20  150.79   19.75
+       86        789T 789T N   CA   6204 6205  167.24  149.80                  -42.10
+       87 114715 789T 790N C   N    6209 6211   73.04   55.90   79.56    4.40  -63.20  136.27   20.77
+       87        790N 790N N   CA   6211 6212  -38.19   39.50                  -41.10
+       88 114733 807Y 808Q C   N    6374 6376   66.01   55.10   11.37    1.18 -121.10 -158.96    9.69
+       88        808Q 808Q N   CA   6376 6377   37.10   40.30                  139.70
+       89 114743 817K 818G C   N    6453 6455  -62.40  -62.40    4.31    0.64   82.20  151.56   11.45
+       89        818G 818G N   CA   6455 6456  -36.89  -41.20                    8.50
+       90 114776 850P 851Q C   N    6726 6728 -102.61  -63.80   74.91    9.61  -63.80   74.91    9.61
+       90        851Q 851Q N   CA   6728 6729   23.77  -40.30                  -40.30
+       91 114777 851Q 852L C   N    6735 6737   75.53   60.20   34.10    1.18  -63.50  144.77   26.37
+       91        852L 852L N   CA   6737 6738   -0.86   29.60                  -41.20
+       92 114779 853G 854G C   N    6747 6749 -149.23 -167.20   21.82    0.39   82.20 -159.59   15.07
+       92        854G 854G N   CA   6749 6750  162.23  174.60                    8.50
+       93 114784 858P 859T C   N    6789 6791   54.32   55.90   10.26    0.84  -63.20  137.54   23.70
+       93        859T 859T N   CA   6791 6792   29.36   39.50                  -42.10
+       94 114785 859T 860G C   N    6796 6798 -112.58  -80.20   58.61    3.83   82.20 -157.70   15.80
+       94        860G 860G N   CA   6798 6799  125.24  174.10                    8.50
+       95 114792 866P 867L C   N    6845 6847  -71.35  -63.50   83.21   12.02  -70.70   94.36    7.12
+       95        867L 867L N   CA   6847 6848 -124.04  -41.20                  141.60
+       96 114818 892M 893E C   N    7040 7042   74.74   54.60   22.69    1.92  -63.60  156.07   26.82
+       96        893E 893E N   CA   7042 7043   31.94   42.40                  -40.30
+       97 114855 929S 930D C   N    7342 7344   34.86  -70.90  115.76    9.70  -63.30  157.09   17.10
+       97        930D 930D N   CA   7344 7345 -162.64  150.30                  -40.00
+       98 114896 970K 971H C   N    7668 7670 -162.17 -125.60   76.34    3.41  -63.20  151.04   16.58
+       98        971H 971H N   CA   7670 7671   71.79  138.80                  -42.30
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+       99       1000G1000G N   CA   7944 7945 -169.83  174.10                    8.50
+      100 1149261002M1003L C   N    7961 7963  -71.48  -70.70    9.17    0.66  -63.50  168.25   23.83
+      100       1003L1003L N   CA   7963 7964  150.73  141.60                  -41.20
+      101 1149271003L1004A C   N    7969 7971  -70.94  -68.20    3.50    0.22  -62.50  171.83   28.58
+      101       1004A1004A N   CA   7971 7972  147.48  145.30                  -40.90
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+      102       1005T1005T N   CA   7976 7977 -130.89  149.80                  -42.10
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+      103       1006R1006R N   CA   7983 7984  153.27  141.90                  -41.10
+      104 1149311007V1008F C   N    7999 8001 -146.93 -124.20   63.91    2.37  -63.20  140.37   24.56
+      104       1008F1008F N   CA   8001 8002 -156.97  143.30                  -44.30
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+      105       1009S1009S N   CA   8012 8013 -170.68  152.40                  -35.00
+      106 1149331009S1010L C   N    8016 8018  -57.11  -70.70   13.75    1.18  -63.50  179.39   24.55
+      106       1010L1010L N   CA   8018 8019  139.52  141.60                  -41.20
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+      107       1012G1012G N   CA   8033 8034  141.75 -166.10                    8.50
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+      108       1013K1013K N   CA   8037 8038  156.59  139.10                  -40.80
+      109 1149371013K1014R C   N    8044 8046 -101.77 -125.20   48.00    1.71  -63.00  145.08   17.33
+      109       1014R1014R N   CA   8046 8047   98.70  140.60                  -41.10
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+      110       1015A1015A N   CA   8057 8058  136.99  147.00                  -40.90
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+      111       1017S1017S N   CA   8070 8071  134.81  151.20                  -35.00
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+      112       1023R1023R N   CA   8109 8110 -139.30  140.60                  -41.10
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+      113       1025H1025H N   CA   8125 8126  124.41  138.80                  -42.30
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+      114       1032E1032E N   CA   8179 8180   37.53  -40.30                  -40.30
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+      115       1071W1071W N   CA   8492 8493  156.28  139.00                  -44.20
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+      119       1128G1128G N   CA   8970 8971  149.26  174.10                    8.50
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+      123       1165K1165K N   CA   9274 9275   32.66   38.60                  -40.80
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+      125       1173G1173G N   CA   9349 9350  169.61  174.60                    8.50
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+      126       1174A1174A N   CA   9353 9354  168.41  147.00                  -40.90
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+      127       1175A1175A N   CA   9358 9359  144.37  145.30                  -40.90
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+      128       1176L1176L N   CA   9363 9364   98.75  132.50                  -41.20
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+      129       1177R1177R N   CA   9371 9372  142.98  140.60                  -41.10
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+      133       1183A1183A N   CA   9416 9417  148.03  147.00                  -40.90
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+      134       1184T1184T N   CA   9421 9422  147.50  143.50                  -42.10
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+      135       1185T1185T N   CA   9428 9429  122.11  149.80                  -42.10
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+      136       1186R1186R N   CA   9435 9436 -160.42  140.60                  -41.10
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+      137       1187A1187A N   CA   9446 9447  169.98  147.00                  -40.90
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+      138       1188D1188D N   CA   9451 9452   84.91  114.20                  -40.00
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+      139       1190R1190R N   CA   9466 9467  138.32  140.60                  -41.10
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+      141       1193L1193L N   CA   9489 9490  146.65  141.60                  -41.20
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+      142       1194H1194H N   CA   9497 9498  127.57  138.80                  -42.30
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+      330       1961E1961E N   CA  1560215603 -173.51  136.80                  -40.30
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+      332       1963K1963K N   CA  1561515616   29.25   38.60                  -40.80
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+      624       3843Q3843Q N   CA  3057330574    9.92  -40.30                  -40.30
+      625 1177273843Q3844V C   N   3058030582   66.79   55.90   15.53    0.92 -125.40 -156.63   11.07
+      625       3844V3844V N   CA  3058230583   28.42   39.50                  143.30
+      626 1177313847E3848W C   N   3060830610   55.34   58.80   26.72    1.17  -63.00  157.35   27.23
+      626       3848W3848W N   CA  3061030611   59.50   33.00                  -44.20
+      627 1177453861W3862R C   N   3072630728  -72.76  -72.10    3.19    0.26  -63.00 -179.86   23.69
+      627       3862R3862R N   CA  3072830729  138.77  141.90                  -41.10
+      628 1177463862R3863N C   N   3073730739 -124.35 -119.90    5.18    0.27  -63.20 -174.19   20.51
+      628       3863N3863N N   CA  3073930740  134.36  137.00                  -41.10
+      629 1177473865M3866L C   N   3076330765  -75.72  -70.70   17.65    1.16  -63.50  160.74   23.04
+      629       3866L3866L N   CA  3076530766  158.52  141.60                  -41.20
+      630 1177493867G3868Q C   N   3077530777  -61.37  -73.00   16.98    1.31  -63.80  166.64   24.38
+      630       3868Q3868Q N   CA  3077730778  153.07  140.70                  -40.30
+      631 1177503868Q3869S C   N   3078430786  -65.51  -72.40    7.05    0.46  -64.10  174.13   12.70
+      631       3869S3869S N   CA  3078630787  150.88  152.40                  -35.00
+      632 1177523870I3871R C   N   3079830800  -66.15  -72.10    8.92    0.78  -63.00  170.39   23.23
+      632       3871R3871R N   CA  3080030801  148.54  141.90                  -41.10
+      633 1177533871R3872R C   N   3080930811  -65.94  -72.10   18.62    1.30  -63.00  165.45   22.15
+      633       3872R3872R N   CA  3081130812  124.33  141.90                  -41.10
+      634 1177543872R3873F C   N   3082030822 -163.41 -124.20   47.49    1.23  -63.20  176.75   30.69
+      634       3873F3873F N   CA  3082230823  170.11  143.30                  -44.30
+      635 1177553873F3874T C   N   3083130833 -102.60 -124.80   49.74    1.58  -63.20  146.48   16.50
+      635       3874T3874T N   CA  3083330834   98.98  143.50                  -42.10
+      636 1177563874T3875T C   N   3083830840 -143.57 -124.80   25.72    0.84  -63.20  176.22   27.81
+      636       3875T3875T N   CA  3084030841  161.08  143.50                  -42.10
+      637 1177573875T3876S C   N   3084530847 -122.02 -136.60   33.55    1.33  -64.10  166.38   10.26
+      637       3876S3876S N   CA  3084730848  120.97  151.20                  -35.00
+      638 1177603878V3879R C   N   3086530867 -123.98 -125.20    6.76    0.30  -63.00 -174.64   21.67
+      638       3879R3879R N   CA  3086730868  133.95  140.60                  -41.10
+      639 1177613879R3880R C   N   3087630878 -125.81 -125.20   13.11    0.65  -63.00  179.92   20.90
+      639       3880R3880R N   CA  3087830879  127.51  140.60                  -41.10
+      640 1177663884E3885E C   N   3092430926   86.92   54.60  109.43   10.98  -63.60 -130.88   26.91
+      640       3885E3885E N   CA  3092630927  146.95   42.40                  -40.30
+      641 1177673885E3886G C   N   3093330935   45.20   78.70   35.20    1.45   82.20  167.92    9.96
+      641       3886G3886G N   CA  3093530936 -155.30 -166.10                    8.50
+      642 1177703888G3889K C   N   3094830950  -96.75 -118.00   92.32    4.15  -62.90   96.21   11.15
+      642       3889K3889K N   CA  3095030951   49.26  139.10                  -40.80
+      643 1178073925L3926K C   N   3124931251 -144.35 -118.00   33.82    1.15   56.60 -159.73   25.19
+      643       3926K3926K N   CA  3125131252  160.30  139.10                   38.60
+      644 1178083928M3929S C   N   3127431276  -70.36  -72.40   16.17    1.02  -64.10  156.68   11.73
+      644       3929S3929S N   CA  3127631277  168.45  152.40                  -35.00
+      645 1178103930V3931L C   N   3128731289 -114.86 -108.50   41.09    2.28  -63.50  142.67   17.65
+      645       3931L3931L N   CA  3128931290   91.90  132.50                  -41.20
+      646 1178113931L3932T C   N   3129531297 -143.54 -124.80   19.49    0.88  -63.20 -172.84   29.24
+      646       3932T3932T N   CA  3129731298  148.86  143.50                  -42.10
+      647 1178133933P3934L C   N   3130931311 -149.04 -108.50   40.68    1.90  -63.50 -163.37   24.12
+      647       3934L3934L N   CA  3131131312  135.84  132.50                  -41.20
+      648 1178143934L3935L C   N   3131731319 -155.83 -108.50   51.18    2.27  -63.50 -169.33   32.16
+      648       3935L3935L N   CA  3131931320  151.98  132.50                  -41.20
+      649 1178153935L3936L C   N   3132531327 -126.53 -108.50   18.27    0.84  -63.50 -172.43   23.31
+      649       3936L3936L N   CA  3132731328  135.47  132.50                  -41.20
+      650 1178163936L3937R C   N   3133331335  -69.19  -72.10   10.34    0.73  -63.00  173.18   22.99
+      650       3937R3937R N   CA  3133531336  131.98  141.90                  -41.10
+      651 1178173937R3938G C   N   3134431346 -120.08  -80.20   52.84    3.80   78.70  170.17    6.93
+      651       3938G3938G N   CA  3134631347  139.43  174.10                 -166.10
+      652 1178193939L3940T C   N   3135631358  -79.78  -78.10   20.47    0.93  -63.20  172.30   21.04
+      652       3940T3940T N   CA  3135831359  129.40  149.80                  -42.10
+      653 1178233943A3944R C   N   3137831380 -152.86  -63.00   91.05   15.88  -63.00   91.05   15.88
+      653       3944R3944R N   CA  3138031381  -55.79  -41.10                  -41.10
+      654 1178253945R3946L C   N   3140031402  -70.83  -70.70   39.54    2.99  -63.50  137.85   19.57
+      654       3946L3946L N   CA  3140231403 -178.86  141.60                  -41.20
+      655 1178263946L3947P C   N   3140831410  -72.14  -58.70   24.59    1.47  -64.50  157.30   12.15
+      655       3947P3947P N   CA  3141031411   -9.91  -30.50                  147.20
+      656 1178273947P3948V C   N   3141531417  -62.25  -62.40    3.05    0.40 -125.40 -171.74   10.55
+      656       3948V3948V N   CA  3141731418  -39.35  -42.40                  143.30
+      657 1178293949P3950R C   N   3142931431   43.49   57.30   38.50    1.86  -72.10  134.09    8.88
+      657       3950R3950R N   CA  3143131432   73.94   38.00                  141.90
+      658 1178363956L3957P C   N   3148631488  -67.50  -58.70   17.87    1.05  -64.50  162.17   12.26
+      658       3957P3957P N   CA  3148831489  -14.94  -30.50                  147.20
+      659 1178393959E3960G C   N   3150931511   86.00   82.20    4.98    0.39  -62.40  157.55   29.64
+      659       3960G3960G N   CA  3151131512   11.72    8.50                  -41.20
+      660 1178413961K3962L C   N   3152231524 -108.06 -108.50   38.37    2.07  -63.50  142.48   17.79
+      660       3962L3962L N   CA  3152431525   94.13  132.50                  -41.20
+      661 1178433963G3964I C   N   3153431536  -61.34  -63.40    2.82    0.53 -120.60 -178.10    8.26
+      661       3964I3964I N   CA  3153631537  -41.68  -43.60                  130.30
+      662 1178443964I3965M C   N   3154231544  111.82 -125.60  144.61    4.29  -63.40 -157.12   29.52
+      662       3965M3965M N   CA  3154431545 -142.79  140.50                  -40.50
+      663 1178733993R3994R C   N   3177131773  -57.04  -72.10   19.56    1.27  -63.00  170.63   23.45
+      663       3994R3994R N   CA  3177331774  129.42  141.90                  -41.10
+    
+    
+    report______> Distribution of short non-bonded contacts:
+    
+    
+    DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
+    DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
+    FREQUENCY:     0    0    0    0   10  290  402 2478 3299 4417 3808 4620 5824 6048 5636
+    
+    
+    << end of ENERGY.
+    
+    >> Summary of successfully produced models:
+    Filename                          molpdf
+    ----------------------------------------
+    9606.B99990001.pdb           20600.91211
+    
+
+
+
+```python
+r=m.residues[0]
+```
+
+
+```python
+r.code
+```
+
+
+
+
+    'I'
+
+
+
+
+```python
+
+```
