Starting phenix.real_space_refine
on Wed Jun  3 21:12:37 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9pik_71670/06_2026/9pik_71670_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9pik_71670/06_2026/9pik_71670.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9pik_71670/06_2026/9pik_71670_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9pik_71670/06_2026/9pik_71670_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9pik_71670/06_2026/9pik_71670.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9pik_71670/06_2026/9pik_71670.map"
  }
  resolution = 2.62
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.047
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     K       3      8.98       5
     S      48      5.16       5
     C    5722      2.51       5
     N    1276      2.21       5
     O    1386      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8435
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3998
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 3998
          Classifications: {'peptide': 505}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 20, 'TRANS': 484}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "B"
      Number of atoms: 3998
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 3998
          Classifications: {'peptide': 505}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 20, 'TRANS': 484}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "A"
      Number of atoms: 221
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 221
          Unusual residues: {'  K': 3, 'LMT': 23}
          Classifications: {'undetermined': 26}
          Link IDs: {None: 25}
          Unresolved non-hydrogen bonds: 633
          Unresolved non-hydrogen angles: 909
          Unresolved non-hydrogen dihedrals: 1254
          Unresolved non-hydrogen chiralities: 230
    Chain: "B"
      Number of atoms: 218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 218
          Unusual residues: {'LMT': 23}
          Classifications: {'undetermined': 23}
          Link IDs: {None: 22}
          Unresolved non-hydrogen bonds: 633
          Unresolved non-hydrogen angles: 909
          Unresolved non-hydrogen dihedrals: 1254
          Unresolved non-hydrogen chiralities: 230
  Time building chain proxies: 2.33, per 1000 atoms: 0.28
  Number of scatterers: 8435
  At special positions: 0
  Unit cell: (92.624, 101.721, 124.05, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     K       3     19.00
     S      48     16.00
     O    1386      8.00
     N    1276      7.00
     C    5722      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 339.1 milliseconds
  

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1908

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 2 sheets defined
      80.6% alpha, 1.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 85 through 90
    Processing helix  chain 'A' and resid 91 through 93
      No H-bonds generated for 'chain 'A' and resid 91 through 93'
    Processing helix  chain 'A' and resid 96 through 103
      removed outlier: 3.786A  pdb=" N   LEU A 103 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 121
    Processing helix  chain 'A' and resid 121 through 143
      Proline residue:  A 131  - end of helix
      removed outlier: 3.590A  pdb=" N   ILE A 136 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   VAL A 139 " --> pdb=" O   MET A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 184
    Processing helix  chain 'A' and resid 188 through 216
      removed outlier: 3.627A  pdb=" N   ARG A 216 " --> pdb=" O   PHE A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 257
      removed outlier: 3.530A  pdb=" N   TYR A 255 " --> pdb=" O   ASN A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 272
    Processing helix  chain 'A' and resid 272 through 295
    Processing helix  chain 'A' and resid 299 through 312
    Processing helix  chain 'A' and resid 323 through 351
    Processing helix  chain 'A' and resid 356 through 380
    Processing helix  chain 'A' and resid 384 through 431
      removed outlier: 3.814A  pdb=" N   GLY A 422 " --> pdb=" O   PHE A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 446
    Processing helix  chain 'A' and resid 457 through 500
      Proline residue:  A 473  - end of helix
    Processing helix  chain 'A' and resid 622 through 651
      removed outlier: 4.124A  pdb=" N   GLN A 629 " --> pdb=" O   ALA A 625 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   VAL A 630 " --> pdb=" O   SER A 626 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LYS A 642 " --> pdb=" O   LEU A 638 " (cutoff:3.500A)
      Proline residue:  A 643  - end of helix
    Processing helix  chain 'A' and resid 657 through 662
    Processing helix  chain 'A' and resid 674 through 678
    Processing helix  chain 'A' and resid 681 through 705
      removed outlier: 4.328A  pdb=" N   GLU A 705 " --> pdb=" O   LEU A 701 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 90
    Processing helix  chain 'B' and resid 91 through 93
      No H-bonds generated for 'chain 'B' and resid 91 through 93'
    Processing helix  chain 'B' and resid 96 through 103
      removed outlier: 3.786A  pdb=" N   LEU B 103 " --> pdb=" O   SER B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 121
    Processing helix  chain 'B' and resid 121 through 143
      Proline residue:  B 131  - end of helix
      removed outlier: 3.590A  pdb=" N   ILE B 136 " --> pdb=" O   LEU B 132 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   VAL B 139 " --> pdb=" O   MET B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 184
    Processing helix  chain 'B' and resid 188 through 216
      removed outlier: 3.627A  pdb=" N   ARG B 216 " --> pdb=" O   PHE B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 257
      removed outlier: 3.530A  pdb=" N   TYR B 255 " --> pdb=" O   ASN B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 272
    Processing helix  chain 'B' and resid 272 through 295
    Processing helix  chain 'B' and resid 299 through 312
    Processing helix  chain 'B' and resid 323 through 351
    Processing helix  chain 'B' and resid 356 through 380
    Processing helix  chain 'B' and resid 384 through 431
      removed outlier: 3.814A  pdb=" N   GLY B 422 " --> pdb=" O   PHE B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 446
    Processing helix  chain 'B' and resid 457 through 500
      Proline residue:  B 473  - end of helix
    Processing helix  chain 'B' and resid 622 through 651
      removed outlier: 4.124A  pdb=" N   GLN B 629 " --> pdb=" O   ALA B 625 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   VAL B 630 " --> pdb=" O   SER B 626 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LYS B 642 " --> pdb=" O   LEU B 638 " (cutoff:3.500A)
      Proline residue:  B 643  - end of helix
    Processing helix  chain 'B' and resid 657 through 662
    Processing helix  chain 'B' and resid 674 through 678
    Processing helix  chain 'B' and resid 681 through 705
      removed outlier: 4.329A  pdb=" N   GLU B 705 " --> pdb=" O   LEU B 701 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 154 through 155
      removed outlier: 4.532A  pdb=" N   LYS A 146 " --> pdb=" O   VAL A 155 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 154 through 155
      removed outlier: 4.532A  pdb=" N   LYS B 146 " --> pdb=" O   VAL B 155 " (cutoff:3.500A)

    626 hydrogen bonds defined for protein.
    1866 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.36

  Time building geometry restraints manager: 1.06 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 2406
        1.34 -     1.46: 1316
        1.46 -     1.57: 4780
        1.57 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 8586
  Sorted by residual:
  bond pdb=" CA  SER A 228 "
       pdb=" CB  SER A 228 "
    ideal  model  delta    sigma   weight residual
    1.530  1.467  0.063 1.61e-02 3.86e+03 1.53e+01
  bond pdb=" CA  SER B 228 "
       pdb=" CB  SER B 228 "
    ideal  model  delta    sigma   weight residual
    1.530  1.467  0.063 1.61e-02 3.86e+03 1.53e+01
  bond pdb=" CA  SER B 192 "
       pdb=" CB  SER B 192 "
    ideal  model  delta    sigma   weight residual
    1.530  1.476  0.054 1.56e-02 4.11e+03 1.19e+01
  bond pdb=" CA  SER B 194 "
       pdb=" CB  SER B 194 "
    ideal  model  delta    sigma   weight residual
    1.530  1.477  0.053 1.57e-02 4.06e+03 1.15e+01
  bond pdb=" CA  SER A 194 "
       pdb=" CB  SER A 194 "
    ideal  model  delta    sigma   weight residual
    1.530  1.477  0.053 1.57e-02 4.06e+03 1.15e+01
  ... (remaining 8581 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.06: 11116
        1.06 -     2.12: 226
        2.12 -     3.18: 92
        3.18 -     4.25: 20
        4.25 -     5.31: 16
  Bond angle restraints: 11470
  Sorted by residual:
  angle pdb=" N   GLU A 229 "
        pdb=" CA  GLU A 229 "
        pdb=" C   GLU A 229 "
      ideal   model   delta    sigma   weight residual
     112.54  107.94    4.60 1.22e+00 6.72e-01 1.42e+01
  angle pdb=" N   GLU B 229 "
        pdb=" CA  GLU B 229 "
        pdb=" C   GLU B 229 "
      ideal   model   delta    sigma   weight residual
     112.54  107.98    4.56 1.22e+00 6.72e-01 1.40e+01
  angle pdb=" N   GLY A 230 "
        pdb=" CA  GLY A 230 "
        pdb=" C   GLY A 230 "
      ideal   model   delta    sigma   weight residual
     112.77  108.94    3.83 1.28e+00 6.10e-01 8.96e+00
  angle pdb=" N   GLY B 230 "
        pdb=" CA  GLY B 230 "
        pdb=" C   GLY B 230 "
      ideal   model   delta    sigma   weight residual
     112.77  108.95    3.82 1.28e+00 6.10e-01 8.92e+00
  angle pdb=" CA  VAL A 142 "
        pdb=" C   VAL A 142 "
        pdb=" O   VAL A 142 "
      ideal   model   delta    sigma   weight residual
     121.05  117.96    3.09 1.11e+00 8.12e-01 7.74e+00
  ... (remaining 11465 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.73: 4647
       11.73 -    23.46: 349
       23.46 -    35.18: 100
       35.18 -    46.91: 32
       46.91 -    58.64: 10
  Dihedral angle restraints: 5138
    sinusoidal: 2184
      harmonic: 2954
  Sorted by residual:
  dihedral pdb=" CA  LEU A 680 "
           pdb=" C   LEU A 680 "
           pdb=" N   LYS A 681 "
           pdb=" CA  LYS A 681 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.44   23.56     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" CA  LEU B 680 "
           pdb=" C   LEU B 680 "
           pdb=" N   LYS B 681 "
           pdb=" CA  LYS B 681 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.46   23.54     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" N   MET B 475 "
           pdb=" CA  MET B 475 "
           pdb=" CB  MET B 475 "
           pdb=" CG  MET B 475 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -105.62   45.62     3      1.50e+01 4.44e-03 8.20e+00
  ... (remaining 5135 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1029
       0.050 -    0.099: 230
       0.099 -    0.149: 31
       0.149 -    0.199: 0
       0.199 -    0.248: 2
  Chirality restraints: 1292
  Sorted by residual:
  chirality pdb=" CA  VAL A 162 "
            pdb=" N   VAL A 162 "
            pdb=" C   VAL A 162 "
            pdb=" CB  VAL A 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.69   -0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" CA  VAL B 162 "
            pdb=" N   VAL B 162 "
            pdb=" C   VAL B 162 "
            pdb=" CB  VAL B 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.69   -0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" CA  GLU B 143 "
            pdb=" N   GLU B 143 "
            pdb=" C   GLU B 143 "
            pdb=" CB  GLU B 143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.33e-01
  ... (remaining 1289 not shown)

  Planarity restraints: 1350
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 190 "    0.012 2.00e-02 2.50e+03   2.41e-02 5.82e+00
        pdb=" C   LEU B 190 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   LEU B 190 "    0.016 2.00e-02 2.50e+03
        pdb=" N   VAL B 191 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 190 "   -0.012 2.00e-02 2.50e+03   2.40e-02 5.75e+00
        pdb=" C   LEU A 190 "    0.041 2.00e-02 2.50e+03
        pdb=" O   LEU A 190 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   VAL A 191 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 222 "    0.021 5.00e-02 4.00e+02   3.19e-02 1.63e+00
        pdb=" N   PRO B 223 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO B 223 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 223 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1347 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.80: 2135
        2.80 -     3.39: 9518
        3.39 -     3.97: 15548
        3.97 -     4.56: 22762
        4.56 -     5.14: 33036
  Nonbonded interactions: 82999
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A  96 "
            pdb=" CB  SER A  99 "
     model   vdw
     2.219 3.520
  nonbonded pdb=" NH2 ARG B  96 "
            pdb=" CB  SER B  99 "
     model   vdw
     2.219 3.520
  nonbonded pdb=" OE1 GLU B 229 "
            pdb=" N   SER B 302 "
     model   vdw
     2.497 3.120
  nonbonded pdb=" OE1 GLU A 229 "
            pdb=" N   SER A 302 "
     model   vdw
     2.497 3.120
  nonbonded pdb=" C   SER A 228 "
            pdb=" OG  SER A 228 "
     model   vdw
     2.548 2.616
  ... (remaining 82994 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 82 through 706 or (resid 904 and (name C1 or name C2 or na \ 
me C3 or name C4 or name C5 or name C6 )) or (resid 905 and (name C2 or name C3  \ 
or name C4 or name C5 or name C6 )) or (resid 906 and (name C4 or name C5 or nam \ 
e C6 )) or (resid 907 and (name C3 or name C4 or name C5 or name C6 )) or (resid \ 
 908 and (name C4 or name C5 or name C6 or name C7 or name C8 )) or resid 909 th \ 
rough 912 or (resid 913 and (name C10 or name C11 or name C12 or name C2 or name \ 
 C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or (res \ 
id 914 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or na \ 
me C7 )) or (resid 915 through 916 and (name C2 or name C3 or name C4 or name C5 \ 
 or name C6 or name C7 )) or resid 917 or (resid 918 and (name C4 or name C5 or  \ 
name C6 or name C7 or name C8 or name C9 )) or (resid 919 and (name C10 or name  \ 
C11 or name C12 or name C2 or name C3 or name C4 or name C5 or name C6 or name C \ 
7 or name C8 or name C9 )) or resid 920 or (resid 921 through 923 and (name C3 o \ 
r name C4 or name C5 or name C6 or name C7 or name C8 ))))
  selection = (chain 'B' and (resid 82 through 706 or resid 804 through 805 or (resid 806 and  \ 
(name C4 or name C5 or name C6 )) or (resid 807 and (name C3 or name C4 or name  \ 
C5 or name C6 )) or (resid 808 and (name C4 or name C5 or name C6 or name C7 or  \ 
name C8 )) or (resid 809 and (name C10 or name C11 or name C3 or name C4 or name \ 
 C5 or name C6 or name C7 or name C8 or name C9 )) or (resid 810 and (name C2 or \ 
 name C3 or name C4 or name C5 or name C6 or name C7 or name C8 )) or resid 811  \ 
through 814 or (resid 815 through 816 and (name C2 or name C3 or name C4 or name \ 
 C5 or name C6 or name C7 )) or (resid 817 and (name C1 or name C2 or name C3 or \ 
 name C4 or name C5 or name C6 or name C7 )) or resid 818 through 819 or (resid  \ 
820 and (name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or (r \ 
esid 821 through 823 and (name C3 or name C4 or name C5 or name C6 or name C7 or \ 
 name C8 ))))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.330
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:7.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   8586  Z= 0.223
  Angle     :  0.485   5.307  11470  Z= 0.275
  Chirality :  0.040   0.248   1292
  Planarity :  0.004   0.032   1350
  Dihedral  :  9.789  58.638   3230
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.24), residues: 1002
  helix:  0.64 (0.17), residues: 782
  sheet:  None (None), residues: 0
  loop :  0.00 (0.43), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  96 
 TYR   0.012   0.001   TYR B 189 
 PHE   0.007   0.001   PHE B 122 
 TRP   0.005   0.001   TRP A 661 
 HIS   0.001   0.001   HIS B 631 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00425 /  0.22 ( 8586)
  covalent geometry    : angle       0.48544 /  0.27 (11470)
  hydrogen bonds       : bond        0.20030 / 13.51 (  626)
  hydrogen bonds       : angle       6.12334 /  4.40 ( 1866)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 ASN cc_start: 0.9030 (t0) cc_final: 0.8818 (t0)
REVERT: A  268 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7779 (tm-30)
REVERT: A  402 ARG cc_start: 0.7554 (ttt180) cc_final: 0.7183 (ttm170)
REVERT: A  475 MET cc_start: 0.8641 (mmm) cc_final: 0.8426 (tpt)
REVERT: A  487 TYR cc_start: 0.7835 (t80) cc_final: 0.7478 (t80)
REVERT: A  488 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8047 (pt0)
REVERT: A  492 ASP cc_start: 0.6802 (t70) cc_final: 0.6401 (m-30)
REVERT: B  176 ASN cc_start: 0.9042 (t0) cc_final: 0.8835 (t0)
REVERT: B  268 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7855 (tm-30)
REVERT: B  402 ARG cc_start: 0.7563 (ttt180) cc_final: 0.7201 (ttm170)
REVERT: B  475 MET cc_start: 0.8657 (mmm) cc_final: 0.8405 (tpt)
REVERT: B  487 TYR cc_start: 0.7824 (t80) cc_final: 0.7467 (t80)
REVERT: B  488 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8063 (pt0)
REVERT: B  492 ASP cc_start: 0.6831 (t70) cc_final: 0.6427 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.7171
  time to fit residues: 73.2876
Evaluate side-chains
  64 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0970
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   overall best weight:    0.6978

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 222 ASN
A 270 GLN
B 222 ASN
B 270 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.091213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.069125 restraints weight = 17217.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 2.46
r_work: 0.2860 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.1475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8586  Z= 0.127
  Angle     :  0.489   5.094  11470  Z= 0.259
  Chirality :  0.039   0.137   1292
  Planarity :  0.004   0.029   1350
  Dihedral  :  7.624  56.944   1380
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  :  5.02 %
    Favored  : 92.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.10 (0.26), residues: 1002
  helix:  2.54 (0.17), residues: 784
  sheet:  None (None), residues: 0
  loop :  0.23 (0.44), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  96 
 TYR   0.016   0.001   TYR B 487 
 PHE   0.007   0.001   PHE B 464 
 TRP   0.007   0.001   TRP A 115 
 HIS   0.002   0.000   HIS A 390 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.13 ( 8586)
  covalent geometry    : angle       0.48903 /  0.26 (11470)
  hydrogen bonds       : bond        0.05390 /  3.65 (  626)
  hydrogen bonds       : angle       3.81926 /  2.78 ( 1866)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A  222 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8132 (p0)
REVERT: A  274 MET cc_start: 0.8115 (tpt) cc_final: 0.7709 (tpt)
REVERT: A  488 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8390 (mm-30)
REVERT: A  492 ASP cc_start: 0.7179 (t70) cc_final: 0.6834 (m-30)
REVERT: B  222 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8127 (p0)
REVERT: B  274 MET cc_start: 0.8113 (tpt) cc_final: 0.7698 (tpt)
REVERT: B  488 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8432 (mm-30)
REVERT: B  492 ASP cc_start: 0.7166 (t70) cc_final: 0.6856 (m-30)
  outliers start: 19
  outliers final: 4
  residues processed: 82
  average time/residue: 0.5786
  time to fit residues: 50.6176
Evaluate side-chains
  63 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain B residue  222 ASN
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  697 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 72 optimal weight:    0.5980
   chunk 17 optimal weight:    0.3980
   chunk 95 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 75 optimal weight:    3.9990
   chunk 99 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 176 ASN
A 222 ASN
A 270 GLN
B 176 ASN
B 222 ASN
B 270 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.091771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.069499 restraints weight = 17012.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 2.47
r_work: 0.2865 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2742 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   8586  Z= 0.115
  Angle     :  0.452   5.141  11470  Z= 0.238
  Chirality :  0.038   0.134   1292
  Planarity :  0.004   0.032   1350
  Dihedral  :  6.907  58.575   1380
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  :  5.14 %
    Favored  : 91.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.74 (0.26), residues: 1002
  helix:  3.03 (0.18), residues: 784
  sheet:  None (None), residues: 0
  loop :  0.31 (0.44), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  96 
 TYR   0.015   0.001   TYR B 439 
 PHE   0.007   0.001   PHE A 463 
 TRP   0.005   0.001   TRP B 115 
 HIS   0.001   0.000   HIS A 390 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.12 ( 8586)
  covalent geometry    : angle       0.45171 /  0.24 (11470)
  hydrogen bonds       : bond        0.04478 /  3.04 (  626)
  hydrogen bonds       : angle       3.57330 /  2.59 ( 1866)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 72
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A  222 ASN cc_start: 0.8842 (OUTLIER) cc_final: 0.8348 (p0)
REVERT: A  229 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7468 (mt-10)
REVERT: A  488 GLU cc_start: 0.8652 (mm-30) cc_final: 0.7996 (pt0)
REVERT: A  492 ASP cc_start: 0.7246 (t70) cc_final: 0.6846 (m-30)
REVERT: A  696 MET cc_start: 0.8756 (pp-130) cc_final: 0.8303 (mtt)
REVERT: A  697 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7800 (ttp)
REVERT: A  704 MET cc_start: 0.9317 (ttm) cc_final: 0.8803 (tmm)
REVERT: B  222 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8350 (p0)
REVERT: B  229 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7509 (mt-10)
REVERT: B  488 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8370 (mm-30)
REVERT: B  492 ASP cc_start: 0.7244 (t70) cc_final: 0.6833 (m-30)
REVERT: B  696 MET cc_start: 0.8732 (pp-130) cc_final: 0.8280 (mtt)
REVERT: B  704 MET cc_start: 0.9318 (ttm) cc_final: 0.8765 (tmm)
  outliers start: 28
  outliers final: 8
  residues processed: 86
  average time/residue: 0.6158
  time to fit residues: 56.3313
Evaluate side-chains
  81 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  341 MET
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  222 ASN
Chi-restraints excluded: chain B residue  229 GLU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain B residue  408 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 82 optimal weight:    5.9990
   chunk 72 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 69 optimal weight:    4.9990
   chunk 68 optimal weight:    5.9990
   chunk 56 optimal weight:    4.9990
   chunk 95 optimal weight:    0.0980
   chunk 92 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    1.7786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 176 ASN
A 222 ASN
A 270 GLN
B 176 ASN
B 222 ASN
B 270 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.090553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.069580 restraints weight = 17275.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 2.34
r_work: 0.2914 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2790 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8788
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   8586  Z= 0.184
  Angle     :  0.499   6.568  11470  Z= 0.259
  Chirality :  0.040   0.135   1292
  Planarity :  0.004   0.030   1350
  Dihedral  :  7.241  57.891   1380
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  :  5.59 %
    Favored  : 90.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.78 (0.26), residues: 1002
  helix:  3.08 (0.18), residues: 784
  sheet:  None (None), residues: 0
  loop :  0.21 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 271 
 TYR   0.016   0.002   TYR B 439 
 PHE   0.010   0.001   PHE B 112 
 TRP   0.007   0.001   TRP A 661 
 HIS   0.002   0.001   HIS A 390 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00437 /  0.18 ( 8586)
  covalent geometry    : angle       0.49851 /  0.26 (11470)
  hydrogen bonds       : bond        0.04609 /  3.13 (  626)
  hydrogen bonds       : angle       3.59620 /  2.60 ( 1866)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 64
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A  222 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8294 (p0)
REVERT: A  229 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.7743 (mt-10)
REVERT: A  488 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8076 (pt0)
REVERT: A  492 ASP cc_start: 0.7281 (t70) cc_final: 0.6936 (m-30)
REVERT: A  696 MET cc_start: 0.8931 (pp-130) cc_final: 0.8571 (mtt)
REVERT: A  704 MET cc_start: 0.9150 (ttm) cc_final: 0.8789 (tmm)
REVERT: B  222 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8275 (p0)
REVERT: B  229 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7754 (mt-10)
REVERT: B  492 ASP cc_start: 0.7273 (t70) cc_final: 0.6908 (m-30)
REVERT: B  696 MET cc_start: 0.8898 (pp-130) cc_final: 0.8549 (mtt)
REVERT: B  704 MET cc_start: 0.9122 (ttm) cc_final: 0.8757 (tmm)
  outliers start: 32
  outliers final: 12
  residues processed: 82
  average time/residue: 0.5985
  time to fit residues: 52.4164
Evaluate side-chains
  75 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 59
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  176 ASN
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  176 ASN
Chi-restraints excluded: chain B residue  222 ASN
Chi-restraints excluded: chain B residue  229 GLU
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  697 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 46 optimal weight:    0.0980
   chunk 72 optimal weight:    0.8980
   chunk 81 optimal weight:    4.9990
   chunk 60 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0670
   chunk 27 optimal weight:    0.9990
   chunk 71 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.5118

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 176 ASN
A 222 ASN
A 270 GLN
B 176 ASN
B 222 ASN
B 270 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.091817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.070508 restraints weight = 17147.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 2.39
r_work: 0.2954 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2830 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8724
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8586  Z= 0.106
  Angle     :  0.454   5.575  11470  Z= 0.237
  Chirality :  0.038   0.136   1292
  Planarity :  0.004   0.031   1350
  Dihedral  :  6.714  55.873   1380
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  :  6.62 %
    Favored  : 90.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.94 (0.26), residues: 1002
  helix:  3.21 (0.18), residues: 784
  sheet:  None (None), residues: 0
  loop :  0.21 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  96 
 TYR   0.015   0.001   TYR B 439 
 PHE   0.008   0.001   PHE A 463 
 TRP   0.005   0.001   TRP B 467 
 HIS   0.001   0.000   HIS A 390 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00222 /  0.11 ( 8586)
  covalent geometry    : angle       0.45359 /  0.24 (11470)
  hydrogen bonds       : bond        0.03975 /  2.69 (  626)
  hydrogen bonds       : angle       3.48855 /  2.52 ( 1866)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 60
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A  222 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8282 (p0)
REVERT: A  488 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8056 (pt0)
REVERT: A  492 ASP cc_start: 0.7325 (t70) cc_final: 0.6991 (m-30)
REVERT: A  696 MET cc_start: 0.8891 (pp-130) cc_final: 0.8518 (mtt)
REVERT: A  697 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7850 (ttp)
REVERT: A  704 MET cc_start: 0.9175 (ttm) cc_final: 0.8828 (tmm)
REVERT: B  222 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8276 (p0)
REVERT: B  488 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7947 (pt0)
REVERT: B  492 ASP cc_start: 0.7312 (t70) cc_final: 0.6968 (m-30)
REVERT: B  696 MET cc_start: 0.8886 (pp-130) cc_final: 0.8523 (mtt)
REVERT: B  704 MET cc_start: 0.9160 (ttm) cc_final: 0.8786 (tmm)
  outliers start: 27
  outliers final: 12
  residues processed: 78
  average time/residue: 0.5887
  time to fit residues: 48.9771
Evaluate side-chains
  73 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  341 MET
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  641 MET
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  222 ASN
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  641 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 20 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 176 ASN
A 222 ASN
A 270 GLN
B 176 ASN
B 222 ASN
B 270 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.092193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.072141 restraints weight = 17059.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 2.30
r_work: 0.2949 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2826 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8732
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8586  Z= 0.120
  Angle     :  0.461   6.055  11470  Z= 0.240
  Chirality :  0.039   0.136   1292
  Planarity :  0.004   0.029   1350
  Dihedral  :  6.616  53.245   1380
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  :  7.08 %
    Favored  : 90.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.02 (0.26), residues: 1002
  helix:  3.27 (0.18), residues: 784
  sheet:  None (None), residues: 0
  loop :  0.21 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  96 
 TYR   0.015   0.001   TYR B 439 
 PHE   0.008   0.001   PHE B 463 
 TRP   0.006   0.001   TRP B 467 
 HIS   0.001   0.000   HIS A 390 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.12 ( 8586)
  covalent geometry    : angle       0.46085 /  0.24 (11470)
  hydrogen bonds       : bond        0.03940 /  2.67 (  626)
  hydrogen bonds       : angle       3.45398 /  2.49 ( 1866)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 59
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A  222 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8269 (p0)
REVERT: A  488 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8072 (pt0)
REVERT: A  492 ASP cc_start: 0.7468 (t70) cc_final: 0.7081 (m-30)
REVERT: A  696 MET cc_start: 0.8911 (pp-130) cc_final: 0.8562 (mtt)
REVERT: A  697 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7842 (ttp)
REVERT: A  704 MET cc_start: 0.9184 (ttm) cc_final: 0.8858 (tmm)
REVERT: B  222 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8250 (p0)
REVERT: B  492 ASP cc_start: 0.7442 (t70) cc_final: 0.7124 (m-30)
REVERT: B  696 MET cc_start: 0.8889 (pp-130) cc_final: 0.8547 (mtt)
REVERT: B  704 MET cc_start: 0.9163 (ttm) cc_final: 0.8818 (tmm)
  outliers start: 25
  outliers final: 15
  residues processed: 75
  average time/residue: 0.5608
  time to fit residues: 45.1141
Evaluate side-chains
  74 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  176 ASN
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  341 MET
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  641 MET
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  176 ASN
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  222 ASN
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  641 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 64 optimal weight:    0.5980
   chunk 87 optimal weight:    6.9990
   chunk 62 optimal weight:    3.9990
   chunk 99 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 55 optimal weight:    0.3980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 176 ASN
A 222 ASN
A 270 GLN
B 176 ASN
B 222 ASN
B 270 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.092533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.072468 restraints weight = 17224.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 2.31
r_work: 0.2953 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2830 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8586  Z= 0.113
  Angle     :  0.460   6.655  11470  Z= 0.239
  Chirality :  0.038   0.136   1292
  Planarity :  0.004   0.028   1350
  Dihedral  :  6.498  51.069   1380
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  :  7.19 %
    Favored  : 90.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.06 (0.26), residues: 1002
  helix:  3.31 (0.18), residues: 784
  sheet:  None (None), residues: 0
  loop :  0.20 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  96 
 TYR   0.015   0.001   TYR B 439 
 PHE   0.008   0.001   PHE A 463 
 TRP   0.006   0.001   TRP A 467 
 HIS   0.001   0.000   HIS A 390 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.11 ( 8586)
  covalent geometry    : angle       0.45973 /  0.24 (11470)
  hydrogen bonds       : bond        0.03829 /  2.59 (  626)
  hydrogen bonds       : angle       3.44546 /  2.48 ( 1866)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 63
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A  222 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8274 (p0)
REVERT: A  488 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8080 (pt0)
REVERT: A  492 ASP cc_start: 0.7428 (t70) cc_final: 0.7024 (m-30)
REVERT: A  696 MET cc_start: 0.8903 (pp-130) cc_final: 0.8543 (mtt)
REVERT: A  704 MET cc_start: 0.9204 (ttm) cc_final: 0.8852 (tmm)
REVERT: B  222 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8260 (p0)
REVERT: B  492 ASP cc_start: 0.7461 (t70) cc_final: 0.7087 (m-30)
REVERT: B  696 MET cc_start: 0.8886 (pp-130) cc_final: 0.8528 (mtt)
REVERT: B  704 MET cc_start: 0.9199 (ttm) cc_final: 0.8792 (tmm)
  outliers start: 24
  outliers final: 15
  residues processed: 77
  average time/residue: 0.5888
  time to fit residues: 48.5751
Evaluate side-chains
  74 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  176 ASN
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  341 MET
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  641 MET
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  222 ASN
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  641 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 84 optimal weight:    0.7980
   chunk 56 optimal weight:    6.9990
   chunk 78 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0670
   chunk 91 optimal weight:    5.9990
   overall best weight:    0.7722

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 176 ASN
A 222 ASN
A 270 GLN
B 176 ASN
B 222 ASN
B 270 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.092304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.071897 restraints weight = 16989.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 2.33
r_work: 0.2956 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8586  Z= 0.116
  Angle     :  0.471   7.055  11470  Z= 0.245
  Chirality :  0.039   0.136   1292
  Planarity :  0.004   0.028   1350
  Dihedral  :  6.408  51.240   1380
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  :  7.65 %
    Favored  : 89.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.04 (0.26), residues: 1002
  helix:  3.29 (0.18), residues: 784
  sheet:  None (None), residues: 0
  loop :  0.18 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  96 
 TYR   0.015   0.001   TYR B 439 
 PHE   0.008   0.001   PHE B 463 
 TRP   0.006   0.001   TRP A 467 
 HIS   0.001   0.000   HIS A 390 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.12 ( 8586)
  covalent geometry    : angle       0.47067 /  0.24 (11470)
  hydrogen bonds       : bond        0.03803 /  2.57 (  626)
  hydrogen bonds       : angle       3.45119 /  2.49 ( 1866)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 58
  time to evaluate  : 0.358 
Fit side-chains
REVERT: A  222 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8366 (p0)
REVERT: A  488 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8109 (pt0)
REVERT: A  492 ASP cc_start: 0.7453 (t70) cc_final: 0.7090 (m-30)
REVERT: A  696 MET cc_start: 0.8896 (pp-130) cc_final: 0.8507 (mtt)
REVERT: A  704 MET cc_start: 0.9204 (ttm) cc_final: 0.8922 (tmm)
REVERT: B  222 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8331 (p0)
REVERT: B  492 ASP cc_start: 0.7494 (t70) cc_final: 0.7109 (m-30)
REVERT: B  696 MET cc_start: 0.8883 (pp-130) cc_final: 0.8519 (mtt)
REVERT: B  697 MET cc_start: 0.8924 (ttp) cc_final: 0.8654 (ttm)
REVERT: B  704 MET cc_start: 0.9203 (ttm) cc_final: 0.8891 (tmm)
  outliers start: 24
  outliers final: 16
  residues processed: 73
  average time/residue: 0.5685
  time to fit residues: 44.5169
Evaluate side-chains
  74 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  176 ASN
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  341 MET
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  641 MET
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  176 ASN
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  222 ASN
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  641 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 84 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 88 optimal weight:    0.5980
   chunk 70 optimal weight:    0.4980
   chunk 4 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 176 ASN
A 222 ASN
A 270 GLN
B 176 ASN
B 222 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.092439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.072039 restraints weight = 17028.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 2.33
r_work: 0.2957 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2834 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.2282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8586  Z= 0.117
  Angle     :  0.481   7.544  11470  Z= 0.249
  Chirality :  0.039   0.136   1292
  Planarity :  0.004   0.028   1350
  Dihedral  :  6.356  51.371   1380
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  :  8.11 %
    Favored  : 89.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.01 (0.26), residues: 1002
  helix:  3.27 (0.18), residues: 784
  sheet:  None (None), residues: 0
  loop :  0.19 (0.44), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  96 
 TYR   0.015   0.001   TYR B 439 
 PHE   0.008   0.001   PHE B 463 
 TRP   0.006   0.001   TRP A 467 
 HIS   0.001   0.000   HIS A 390 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.12 ( 8586)
  covalent geometry    : angle       0.48120 /  0.25 (11470)
  hydrogen bonds       : bond        0.03772 /  2.55 (  626)
  hydrogen bonds       : angle       3.45489 /  2.49 ( 1866)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 58
  time to evaluate  : 0.311 
Fit side-chains
REVERT: A  222 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8362 (p0)
REVERT: A  488 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8113 (pt0)
REVERT: A  492 ASP cc_start: 0.7445 (t70) cc_final: 0.7096 (m-30)
REVERT: A  704 MET cc_start: 0.9206 (ttm) cc_final: 0.8930 (tmm)
REVERT: B  222 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8340 (p0)
REVERT: B  351 VAL cc_start: 0.9077 (t) cc_final: 0.8874 (p)
REVERT: B  492 ASP cc_start: 0.7481 (t70) cc_final: 0.7113 (m-30)
REVERT: B  696 MET cc_start: 0.8897 (pp-130) cc_final: 0.8513 (mtt)
REVERT: B  704 MET cc_start: 0.9198 (ttm) cc_final: 0.8896 (tmm)
  outliers start: 21
  outliers final: 14
  residues processed: 70
  average time/residue: 0.5760
  time to fit residues: 43.2208
Evaluate side-chains
  71 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  176 ASN
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  341 MET
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  641 MET
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  176 ASN
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  222 ASN
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  641 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 9 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 89 optimal weight:    5.9990
   chunk 69 optimal weight:    5.9990
   chunk 85 optimal weight:    0.7980
   chunk 7 optimal weight:    0.4980
   chunk 99 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 76 optimal weight:    0.6980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 176 ASN
A 222 ASN
B 176 ASN
B 222 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.092193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.071711 restraints weight = 17065.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 2.33
r_work: 0.2957 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2834 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.2310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8586  Z= 0.117
  Angle     :  0.479   7.839  11470  Z= 0.249
  Chirality :  0.039   0.136   1292
  Planarity :  0.004   0.028   1350
  Dihedral  :  6.315  51.463   1380
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  :  8.45 %
    Favored  : 89.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.02 (0.26), residues: 1002
  helix:  3.28 (0.18), residues: 784
  sheet:  None (None), residues: 0
  loop :  0.19 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  96 
 TYR   0.015   0.001   TYR B 439 
 PHE   0.008   0.001   PHE B 463 
 TRP   0.006   0.001   TRP B 467 
 HIS   0.001   0.000   HIS A 390 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.12 ( 8586)
  covalent geometry    : angle       0.47869 /  0.25 (11470)
  hydrogen bonds       : bond        0.03753 /  2.53 (  626)
  hydrogen bonds       : angle       3.44995 /  2.49 ( 1866)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 58
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A  222 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8297 (p0)
REVERT: A  351 VAL cc_start: 0.9077 (t) cc_final: 0.8864 (p)
REVERT: A  488 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8120 (pt0)
REVERT: A  492 ASP cc_start: 0.7461 (t70) cc_final: 0.7110 (m-30)
REVERT: A  704 MET cc_start: 0.9205 (ttm) cc_final: 0.8939 (tmm)
REVERT: B  222 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8268 (p0)
REVERT: B  351 VAL cc_start: 0.9077 (t) cc_final: 0.8864 (p)
REVERT: B  492 ASP cc_start: 0.7483 (t70) cc_final: 0.7121 (m-30)
REVERT: B  696 MET cc_start: 0.8913 (pp-130) cc_final: 0.8510 (mtt)
REVERT: B  704 MET cc_start: 0.9201 (ttm) cc_final: 0.8909 (tmm)
  outliers start: 18
  outliers final: 14
  residues processed: 71
  average time/residue: 0.5790
  time to fit residues: 44.0959
Evaluate side-chains
  73 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  176 ASN
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  341 MET
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  641 MET
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  128 CYS
Chi-restraints excluded: chain B residue  176 ASN
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  222 ASN
Chi-restraints excluded: chain B residue  341 MET
Chi-restraints excluded: chain B residue  408 LEU
Chi-restraints excluded: chain B residue  641 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 83 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 56 optimal weight:    4.9990
   chunk 57 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 5 optimal weight:    0.7980
   chunk 94 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 176 ASN
A 222 ASN
B 176 ASN
B 222 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.092380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.071928 restraints weight = 17006.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 2.31
r_work: 0.2963 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2840 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8727
moved from start:          0.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8586  Z= 0.113
  Angle     :  0.486   7.861  11470  Z= 0.250
  Chirality :  0.038   0.136   1292
  Planarity :  0.004   0.028   1350
  Dihedral  :  6.248  51.624   1380
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  :  8.22 %
    Favored  : 89.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.03 (0.26), residues: 1002
  helix:  3.28 (0.18), residues: 784
  sheet:  None (None), residues: 0
  loop :  0.21 (0.44), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  96 
 TYR   0.015   0.001   TYR A 439 
 PHE   0.008   0.001   PHE B 463 
 TRP   0.006   0.001   TRP A 467 
 HIS   0.001   0.000   HIS A 390 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.11 ( 8586)
  covalent geometry    : angle       0.48590 /  0.25 (11470)
  hydrogen bonds       : bond        0.03701 /  2.50 (  626)
  hydrogen bonds       : angle       3.44561 /  2.49 ( 1866)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3103.27 seconds
wall clock time: 53 minutes 41.76 seconds (3221.76 seconds total)