Starting phenix.real_space_refine
on Tue Feb  3 21:09:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9s41_54558/02_2026/9s41_54558.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9s41_54558/02_2026/9s41_54558.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9s41_54558/02_2026/9s41_54558.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9s41_54558/02_2026/9s41_54558.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9s41_54558/02_2026/9s41_54558.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9s41_54558/02_2026/9s41_54558.map"
  }
  resolution = 3.66
  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=   0.000 sd=   0.044
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: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    4612      2.51       5
     N    1068      2.21       5
     O    1159      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6879
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1044
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1044
          Classifications: {'peptide': 138}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 133}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 30
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "B"
      Number of atoms: 1036
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1036
          Classifications: {'peptide': 138}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 4, 'TRANS': 133}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "C"
      Number of atoms: 1043
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1043
          Classifications: {'peptide': 138}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 4, 'TRANS': 133}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 31
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "D"
      Number of atoms: 1036
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1036
          Classifications: {'peptide': 138}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 4, 'TRANS': 133}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "I"
      Number of atoms: 1360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 181, 1360
          Classifications: {'peptide': 181}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 4, 'TRANS': 176}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 62
          Unresolved non-hydrogen angles: 75
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 41
    Chain: "J"
      Number of atoms: 1360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 181, 1360
          Classifications: {'peptide': 181}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 4, 'TRANS': 176}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 62
          Unresolved non-hydrogen angles: 75
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 41
  Time building chain proxies: 1.57, per 1000 atoms: 0.23
  Number of scatterers: 6879
  At special positions: 0
  Unit cell: (68.558, 113.162, 83.426, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      40     16.00
     O    1159      8.00
     N    1068      7.00
     C    4612      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS I  62 " - pdb=" SG  CYS I  72 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J  62 " - pdb=" SG  CYS J  72 " distance=2.03

  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: 0.64
  Conformation dependent library (CDL) restraints added in 272.3 milliseconds
  

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1676

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 2 sheets defined
      75.7% alpha, 4.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 511 through 515
      removed outlier: 3.588A  pdb=" N   LEU A 514 " --> pdb=" O   PHE A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 540
    Processing helix  chain 'A' and resid 568 through 581
    Processing helix  chain 'A' and resid 591 through 626
    Processing helix  chain 'A' and resid 784 through 787
    Processing helix  chain 'A' and resid 788 through 815
      removed outlier: 3.604A  pdb=" N   SER A 814 " --> pdb=" O   PHE A 810 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ARG A 815 " --> pdb=" O   CYS A 811 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 516 through 520
    Processing helix  chain 'B' and resid 523 through 548
    Processing helix  chain 'B' and resid 573 through 586
    Processing helix  chain 'B' and resid 596 through 627
      removed outlier: 3.675A  pdb=" N   VAL B 602 " --> pdb=" O   SER B 598 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 793 through 820
      removed outlier: 3.664A  pdb=" N   PHE B 797 " --> pdb=" O   VAL B 793 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   SER B 819 " --> pdb=" O   PHE B 815 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   ARG B 820 " --> pdb=" O   CYS B 816 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 511 through 515
      removed outlier: 3.577A  pdb=" N   LEU C 514 " --> pdb=" O   PHE C 511 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 518 through 543
      removed outlier: 3.693A  pdb=" N   PHE C 542 " --> pdb=" O   LEU C 538 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   SER C 543 " --> pdb=" O   VAL C 539 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 568 through 581
    Processing helix  chain 'C' and resid 591 through 626
    Processing helix  chain 'C' and resid 784 through 787
    Processing helix  chain 'C' and resid 788 through 815
      removed outlier: 3.558A  pdb=" N   ARG C 815 " --> pdb=" O   CYS C 811 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 516 through 520
    Processing helix  chain 'D' and resid 523 through 548
    Processing helix  chain 'D' and resid 573 through 586
    Processing helix  chain 'D' and resid 596 through 627
      removed outlier: 3.860A  pdb=" N   VAL D 602 " --> pdb=" O   SER D 598 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 789 through 792
    Processing helix  chain 'D' and resid 793 through 820
      removed outlier: 3.762A  pdb=" N   SER D 819 " --> pdb=" O   PHE D 815 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ARG D 820 " --> pdb=" O   CYS D 816 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 7 through 30
    Processing helix  chain 'I' and resid 87 through 101
      removed outlier: 3.843A  pdb=" N   ARG I  98 " --> pdb=" O   LEU I  94 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   THR I  99 " --> pdb=" O   LYS I  95 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ALA I 100 " --> pdb=" O   THR I  96 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 101 through 124
      removed outlier: 4.008A  pdb=" N   MET I 105 " --> pdb=" O   THR I 101 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 129 through 161
      removed outlier: 3.505A  pdb=" N   VAL I 133 " --> pdb=" O   ILE I 129 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 176 through 206
      removed outlier: 3.669A  pdb=" N   ALA I 180 " --> pdb=" O   GLY I 176 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU I 187 " --> pdb=" O   ALA I 183 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 7 through 30
    Processing helix  chain 'J' and resid 87 through 101
      removed outlier: 3.842A  pdb=" N   ARG J  98 " --> pdb=" O   LEU J  94 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   THR J  99 " --> pdb=" O   LYS J  95 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ALA J 100 " --> pdb=" O   THR J  96 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 101 through 124
      removed outlier: 4.008A  pdb=" N   MET J 105 " --> pdb=" O   THR J 101 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 129 through 162
      removed outlier: 3.508A  pdb=" N   VAL J 133 " --> pdb=" O   ILE J 129 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ASN J 162 " --> pdb=" O   ASP J 158 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 176 through 206
      removed outlier: 3.668A  pdb=" N   ALA J 180 " --> pdb=" O   GLY J 176 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LEU J 187 " --> pdb=" O   ALA J 183 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'I' and resid 72 through 74
      removed outlier: 6.350A  pdb=" N   ALA I  53 " --> pdb=" O   PHE I  64 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 72 through 74
      removed outlier: 6.350A  pdb=" N   ALA J  53 " --> pdb=" O   PHE J  64 " (cutoff:3.500A)

    572 hydrogen bonds defined for protein.
    1671 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: 0.84

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2019
        1.34 -     1.46: 1788
        1.46 -     1.58: 3186
        1.58 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 7055
  Sorted by residual:
  bond pdb=" CA  THR J 101 "
       pdb=" C   THR J 101 "
    ideal  model  delta    sigma   weight residual
    1.521  1.534 -0.013 1.17e-02 7.31e+03 1.16e+00
  bond pdb=" CA  THR I 101 "
       pdb=" C   THR I 101 "
    ideal  model  delta    sigma   weight residual
    1.521  1.534 -0.013 1.17e-02 7.31e+03 1.16e+00
  bond pdb=" N   PRO I 102 "
       pdb=" CA  PRO I 102 "
    ideal  model  delta    sigma   weight residual
    1.471  1.482 -0.011 1.32e-02 5.74e+03 7.37e-01
  bond pdb=" CB  VAL I  24 "
       pdb=" CG2 VAL I  24 "
    ideal  model  delta    sigma   weight residual
    1.521  1.493  0.028 3.30e-02 9.18e+02 7.09e-01
  bond pdb=" N   PRO J 102 "
       pdb=" CA  PRO J 102 "
    ideal  model  delta    sigma   weight residual
    1.471  1.482 -0.011 1.32e-02 5.74e+03 6.94e-01
  ... (remaining 7050 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 9422
        1.42 -     2.84: 140
        2.84 -     4.25: 23
        4.25 -     5.67: 9
        5.67 -     7.09: 5
  Bond angle restraints: 9599
  Sorted by residual:
  angle pdb=" CA  LEU I  22 "
        pdb=" CB  LEU I  22 "
        pdb=" CG  LEU I  22 "
      ideal   model   delta    sigma   weight residual
     116.30  123.39   -7.09 3.50e+00 8.16e-02 4.10e+00
  angle pdb=" CA  LEU J  22 "
        pdb=" CB  LEU J  22 "
        pdb=" CG  LEU J  22 "
      ideal   model   delta    sigma   weight residual
     116.30  123.39   -7.09 3.50e+00 8.16e-02 4.10e+00
  angle pdb=" N   VAL A 788 "
        pdb=" CA  VAL A 788 "
        pdb=" C   VAL A 788 "
      ideal   model   delta    sigma   weight residual
     111.88  109.75    2.13 1.06e+00 8.90e-01 4.05e+00
  angle pdb=" C   TRP J  33 "
        pdb=" N   LEU J  34 "
        pdb=" CA  LEU J  34 "
      ideal   model   delta    sigma   weight residual
     121.94  118.41    3.53 1.76e+00 3.23e-01 4.03e+00
  angle pdb=" C   TRP I  33 "
        pdb=" N   LEU I  34 "
        pdb=" CA  LEU I  34 "
      ideal   model   delta    sigma   weight residual
     121.94  118.48    3.46 1.76e+00 3.23e-01 3.86e+00
  ... (remaining 9594 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.07: 3608
       15.07 -    30.14: 270
       30.14 -    45.21: 45
       45.21 -    60.29: 11
       60.29 -    75.36: 5
  Dihedral angle restraints: 3939
    sinusoidal: 1333
      harmonic: 2606
  Sorted by residual:
  dihedral pdb=" CA  PHE C 567 "
           pdb=" C   PHE C 567 "
           pdb=" N   GLY C 568 "
           pdb=" CA  GLY C 568 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.39   16.61     0      5.00e+00 4.00e-02 1.10e+01
  dihedral pdb=" CA  PHE A 567 "
           pdb=" C   PHE A 567 "
           pdb=" N   GLY A 568 "
           pdb=" CA  GLY A 568 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.51   15.49     0      5.00e+00 4.00e-02 9.59e+00
  dihedral pdb=" N   ARG C 590 "
           pdb=" CA  ARG C 590 "
           pdb=" CB  ARG C 590 "
           pdb=" CG  ARG C 590 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -127.53  -52.47     3      1.50e+01 4.44e-03 9.12e+00
  ... (remaining 3936 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 668
       0.027 -    0.054: 308
       0.054 -    0.080: 112
       0.080 -    0.107: 29
       0.107 -    0.134: 15
  Chirality restraints: 1132
  Sorted by residual:
  chirality pdb=" CA  VAL J  61 "
            pdb=" N   VAL J  61 "
            pdb=" C   VAL J  61 "
            pdb=" CB  VAL J  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.47e-01
  chirality pdb=" CA  VAL I  61 "
            pdb=" N   VAL I  61 "
            pdb=" C   VAL I  61 "
            pdb=" CB  VAL I  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.47e-01
  chirality pdb=" CA  PHE I 103 "
            pdb=" N   PHE I 103 "
            pdb=" C   PHE I 103 "
            pdb=" CB  PHE I 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 3.95e-01
  ... (remaining 1129 not shown)

  Planarity restraints: 1156
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 588 "    0.022 5.00e-02 4.00e+02   3.38e-02 1.83e+00
        pdb=" N   PRO C 589 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO C 589 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C 589 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE I 103 "    0.021 5.00e-02 4.00e+02   3.19e-02 1.63e+00
        pdb=" N   PRO I 104 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO I 104 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO I 104 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE J 103 "   -0.021 5.00e-02 4.00e+02   3.19e-02 1.63e+00
        pdb=" N   PRO J 104 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO J 104 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO J 104 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1153 not shown)

  Histogram of nonbonded interaction distances:
        2.54 -     3.01: 4046
        3.01 -     3.48: 7508
        3.48 -     3.96: 10966
        3.96 -     4.43: 12447
        4.43 -     4.90: 19911
  Nonbonded interactions: 54878
  Sorted by model distance:
  nonbonded pdb=" O   SER D 548 "
            pdb=" OG  SER D 548 "
     model   vdw
     2.540 3.040
  nonbonded pdb=" N   LEU I  85 "
            pdb=" N   VAL I  86 "
     model   vdw
     2.630 2.560
  nonbonded pdb=" N   VAL A 788 "
            pdb=" N   ALA A 789 "
     model   vdw
     2.635 2.560
  nonbonded pdb=" N   LEU J  85 "
            pdb=" N   VAL J  86 "
     model   vdw
     2.646 2.560
  nonbonded pdb=" O   SER C 543 "
            pdb=" CA  PRO C 544 "
     model   vdw
     2.648 2.776
  ... (remaining 54873 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 504 through 519 or (resid 520 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 521 through 542 or (resid 543 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 544 through 614 or (resid  \ 
615 and (name N or name CA or name C or name O or name CB or name CG )) or resid \ 
 616 through 624 or (resid 625 and (name N or name CA or name C or name O or nam \ 
e CB or name CG )) or resid 781 through 783 or (resid 784 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 785 through 795 or resid 797 through \ 
 815))
  selection = (chain 'B' and ((resid 509 through 512 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 513 through 547 or (resid 548 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 549 or (resid 570 and (name N or name C \ 
A or name C or name O or name CB )) or resid 571 through 630 or resid 786 throug \ 
h 800 or resid 802 through 820))
  selection = (chain 'C' and (resid 504 through 519 or (resid 520 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 521 through 614 or (resid 615 and (name N  \ 
or name CA or name C or name O or name CB or name CG )) or resid 616 through 624 \ 
 or (resid 625 and (name N or name CA or name C or name O or name CB or name CG  \ 
)) or resid 781 through 783 or (resid 784 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 785 through 795 or resid 797 through 815))
  selection = (chain 'D' and ((resid 509 through 512 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 513 through 547 or (resid 548 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 549 or (resid 570 and (name N or name C \ 
A or name C or name O or name CB )) or resid 571 through 630 or resid 786 throug \ 
h 800 or resid 802 through 820))
}
ncs_group {
  reference = chain 'I'
  selection = chain 'J'
}

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 group one per residue
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:             7.710
  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:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.290
  Find NCS groups from input model:        0.120
  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:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
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      :  0.002   0.028   7057  Z= 0.113
  Angle     :  0.491   7.090   9603  Z= 0.254
  Chirality :  0.037   0.134   1132
  Planarity :  0.004   0.034   1156
  Dihedral  : 11.235  75.357   2257
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  7.96 %
    Favored  : 91.75 %
  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:  4.06 (0.28), residues: 874
  helix:  3.42 (0.19), residues: 662
  sheet:  0.66 (0.72), residues: 60
  loop : -0.03 (0.51), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 600 
 TYR   0.014   0.001   TYR B 798 
 PHE   0.020   0.001   PHE A 527 
 TRP   0.015   0.002   TRP B 579 
 HIS   0.009   0.003   HIS J 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 7055)
  covalent geometry    : angle       0.49111 ( 9599)
  SS BOND              : bond        0.00256 (    2)
  SS BOND              : angle       0.32645 (    4)
  hydrogen bonds       : bond        0.10322 (  572)
  hydrogen bonds       : angle       3.95979 ( 1671)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 208
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  544 PRO cc_start: 0.5230 (Cg_endo) cc_final: 0.4988 (Cg_exo)
REVERT: A  588 SER cc_start: 0.9326 (t) cc_final: 0.8895 (p)
REVERT: A  781 SER cc_start: 0.6432 (p) cc_final: 0.5841 (p)
REVERT: B  595 ARG cc_start: 0.7993 (mtt180) cc_final: 0.7686 (tmt170)
REVERT: C  576 SER cc_start: 0.9019 (m) cc_final: 0.8791 (m)
REVERT: C  588 SER cc_start: 0.9213 (t) cc_final: 0.8831 (p)
REVERT: D  595 ARG cc_start: 0.8073 (mtt180) cc_final: 0.7766 (tmt170)
REVERT: I   22 LEU cc_start: 0.8641 (tp) cc_final: 0.8040 (mt)
REVERT: I  189 LYS cc_start: 0.8662 (mttm) cc_final: 0.8462 (mttm)
REVERT: J   22 LEU cc_start: 0.8653 (tp) cc_final: 0.8040 (mt)
  outliers start: 2
  outliers final: 1
  residues processed: 210
  average time/residue: 0.0652
  time to fit residues: 18.5640
Evaluate side-chains
  155 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 154
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   35 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0170
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.7020

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

Flipped N/Q/H residues before XYZ refinement:
A 583 GLN
D 588 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.184779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.153318 restraints weight = 9231.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.157650 restraints weight = 4837.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.160428 restraints weight = 3293.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.162161 restraints weight = 2607.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.162864 restraints weight = 2257.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7057  Z= 0.148
  Angle     :  0.494   6.793   9603  Z= 0.260
  Chirality :  0.039   0.149   1132
  Planarity :  0.003   0.037   1156
  Dihedral  :  3.416  35.156    958
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 16.50 %
    Favored  : 80.90 %
  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:  4.37 (0.28), residues: 874
  helix:  3.65 (0.19), residues: 664
  sheet:  0.24 (0.89), residues: 40
  loop :  0.21 (0.47), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 595 
 TYR   0.010   0.001   TYR I  35 
 PHE   0.017   0.001   PHE A 511 
 TRP   0.008   0.001   TRP D 607 
 HIS   0.007   0.002   HIS J 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 7055)
  covalent geometry    : angle       0.49376 ( 9599)
  SS BOND              : bond        0.00229 (    2)
  SS BOND              : angle       0.52560 (    4)
  hydrogen bonds       : bond        0.04277 (  572)
  hydrogen bonds       : angle       3.41428 ( 1671)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 157
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A  588 SER cc_start: 0.9353 (t) cc_final: 0.9038 (p)
REVERT: B  528 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7332 (tmm)
REVERT: B  591 ASP cc_start: 0.7504 (p0) cc_final: 0.7066 (p0)
REVERT: I   36 MET cc_start: 0.7987 (ptp) cc_final: 0.7749 (ptp)
REVERT: I   54 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.5756 (pp)
REVERT: J   36 MET cc_start: 0.8104 (ptp) cc_final: 0.7772 (ptp)
REVERT: J   54 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.5804 (pp)
  outliers start: 18
  outliers final: 8
  residues processed: 168
  average time/residue: 0.0581
  time to fit residues: 13.6521
Evaluate side-chains
  152 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 141
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  528 MET
Chi-restraints excluded: chain I residue   12 LEU
Chi-restraints excluded: chain I residue   28 VAL
Chi-restraints excluded: chain I residue   35 TYR
Chi-restraints excluded: chain I residue   54 LEU
Chi-restraints excluded: chain I residue  146 VAL
Chi-restraints excluded: chain J residue   28 VAL
Chi-restraints excluded: chain J residue   35 TYR
Chi-restraints excluded: chain J residue   54 LEU
Chi-restraints excluded: chain J residue  110 LEU
Chi-restraints excluded: chain J residue  146 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 56 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0070
   chunk 82 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 69 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.5598

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.177958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.148376 restraints weight = 9022.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.152670 restraints weight = 4674.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.155130 restraints weight = 3180.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.156987 restraints weight = 2555.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.157505 restraints weight = 2193.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7057  Z= 0.126
  Angle     :  0.455   6.212   9603  Z= 0.237
  Chirality :  0.037   0.143   1132
  Planarity :  0.003   0.038   1156
  Dihedral  :  3.318  36.003    958
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.08 %
    Favored  : 80.17 %
  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:  4.62 (0.28), residues: 874
  helix:  3.89 (0.19), residues: 664
  sheet:  0.06 (0.88), residues: 40
  loop :  0.11 (0.45), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 595 
 TYR   0.008   0.001   TYR I 152 
 PHE   0.009   0.001   PHE A 511 
 TRP   0.007   0.001   TRP I 177 
 HIS   0.006   0.002   HIS J 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7055)
  covalent geometry    : angle       0.45468 ( 9599)
  SS BOND              : bond        0.00135 (    2)
  SS BOND              : angle       0.36337 (    4)
  hydrogen bonds       : bond        0.03921 (  572)
  hydrogen bonds       : angle       3.26474 ( 1671)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  588 SER cc_start: 0.9342 (t) cc_final: 0.8987 (p)
REVERT: B  591 ASP cc_start: 0.7535 (p0) cc_final: 0.7039 (p0)
REVERT: I   22 LEU cc_start: 0.8630 (tp) cc_final: 0.8119 (mt)
REVERT: I   54 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.5850 (pp)
REVERT: I  195 MET cc_start: 0.8461 (mpp) cc_final: 0.8221 (mpp)
REVERT: J   22 LEU cc_start: 0.8625 (tp) cc_final: 0.8118 (mt)
REVERT: J   36 MET cc_start: 0.8062 (ptp) cc_final: 0.7751 (ptp)
REVERT: J   52 MET cc_start: 0.5355 (ptt) cc_final: 0.5010 (ptt)
REVERT: J   54 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.5778 (pp)
REVERT: J  198 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.7944 (m-10)
  outliers start: 19
  outliers final: 10
  residues processed: 156
  average time/residue: 0.0686
  time to fit residues: 14.8272
Evaluate side-chains
  155 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 142
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  511 SER
Chi-restraints excluded: chain D residue  808 MET
Chi-restraints excluded: chain D residue  816 CYS
Chi-restraints excluded: chain I residue   28 VAL
Chi-restraints excluded: chain I residue   35 TYR
Chi-restraints excluded: chain I residue   54 LEU
Chi-restraints excluded: chain I residue   99 THR
Chi-restraints excluded: chain I residue  110 LEU
Chi-restraints excluded: chain J residue   28 VAL
Chi-restraints excluded: chain J residue   35 TYR
Chi-restraints excluded: chain J residue   54 LEU
Chi-restraints excluded: chain J residue   99 THR
Chi-restraints excluded: chain J residue  198 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 78 optimal weight:    0.8980
   chunk 68 optimal weight:    0.5980
   chunk 54 optimal weight:    3.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
I 169 GLN
J 169 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.171808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.141448 restraints weight = 9288.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.145573 restraints weight = 4763.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.148206 restraints weight = 3278.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.149574 restraints weight = 2626.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.150594 restraints weight = 2322.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.2350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7057  Z= 0.172
  Angle     :  0.496   7.182   9603  Z= 0.262
  Chirality :  0.039   0.145   1132
  Planarity :  0.003   0.038   1156
  Dihedral  :  3.423  37.560    958
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.95 %
    Favored  : 79.16 %
  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:  4.52 (0.28), residues: 874
  helix:  3.81 (0.19), residues: 662
  sheet: -0.03 (0.88), residues: 40
  loop :  0.15 (0.45), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 595 
 TYR   0.011   0.001   TYR J 152 
 PHE   0.008   0.001   PHE I  64 
 TRP   0.005   0.001   TRP I 177 
 HIS   0.005   0.002   HIS J  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 7055)
  covalent geometry    : angle       0.49570 ( 9599)
  SS BOND              : bond        0.00155 (    2)
  SS BOND              : angle       0.41373 (    4)
  hydrogen bonds       : bond        0.04397 (  572)
  hydrogen bonds       : angle       3.40555 ( 1671)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 155
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  588 SER cc_start: 0.9358 (t) cc_final: 0.8960 (p)
REVERT: B  591 ASP cc_start: 0.7641 (p0) cc_final: 0.7172 (p0)
REVERT: D  595 ARG cc_start: 0.8001 (mtt180) cc_final: 0.7568 (tmt170)
REVERT: I   22 LEU cc_start: 0.8598 (tp) cc_final: 0.8086 (mt)
REVERT: I   54 LEU cc_start: 0.6562 (OUTLIER) cc_final: 0.5833 (pp)
REVERT: I  112 PHE cc_start: 0.7966 (t80) cc_final: 0.7710 (m-80)
REVERT: J   22 LEU cc_start: 0.8629 (tp) cc_final: 0.8123 (mt)
REVERT: J   54 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.5818 (pp)
REVERT: J  112 PHE cc_start: 0.7976 (t80) cc_final: 0.7726 (m-80)
REVERT: J  198 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.7916 (m-10)
  outliers start: 20
  outliers final: 12
  residues processed: 169
  average time/residue: 0.0649
  time to fit residues: 15.1447
Evaluate side-chains
  168 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 153
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  512 SER
Chi-restraints excluded: chain B residue  816 CYS
Chi-restraints excluded: chain D residue  511 SER
Chi-restraints excluded: chain D residue  517 SER
Chi-restraints excluded: chain D residue  545 SER
Chi-restraints excluded: chain D residue  808 MET
Chi-restraints excluded: chain I residue   28 VAL
Chi-restraints excluded: chain I residue   35 TYR
Chi-restraints excluded: chain I residue   54 LEU
Chi-restraints excluded: chain I residue  110 LEU
Chi-restraints excluded: chain J residue   28 VAL
Chi-restraints excluded: chain J residue   35 TYR
Chi-restraints excluded: chain J residue   54 LEU
Chi-restraints excluded: chain J residue  110 LEU
Chi-restraints excluded: chain J residue  198 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   chunk 60 optimal weight:    0.0870
   chunk 21 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 27 optimal weight:    0.4980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A 583 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.174442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.143844 restraints weight = 9193.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.147980 restraints weight = 4852.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.150611 restraints weight = 3337.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.152158 restraints weight = 2674.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.152966 restraints weight = 2346.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.2424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7057  Z= 0.121
  Angle     :  0.456   7.193   9603  Z= 0.234
  Chirality :  0.037   0.141   1132
  Planarity :  0.003   0.040   1156
  Dihedral  :  3.295  37.767    958
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 18.81 %
    Favored  : 79.31 %
  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:  4.76 (0.28), residues: 874
  helix:  3.98 (0.19), residues: 666
  sheet: -0.02 (0.87), residues: 40
  loop :  0.18 (0.46), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 600 
 TYR   0.009   0.001   TYR I  35 
 PHE   0.017   0.001   PHE D 815 
 TRP   0.006   0.001   TRP J 177 
 HIS   0.005   0.002   HIS J 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7055)
  covalent geometry    : angle       0.45611 ( 9599)
  SS BOND              : bond        0.00076 (    2)
  SS BOND              : angle       0.27592 (    4)
  hydrogen bonds       : bond        0.03836 (  572)
  hydrogen bonds       : angle       3.17547 ( 1671)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 150
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  588 SER cc_start: 0.9328 (t) cc_final: 0.8914 (p)
REVERT: B  591 ASP cc_start: 0.7677 (p0) cc_final: 0.7213 (p0)
REVERT: I   22 LEU cc_start: 0.8580 (tp) cc_final: 0.8077 (mt)
REVERT: I   54 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.5942 (pp)
REVERT: J   22 LEU cc_start: 0.8589 (tp) cc_final: 0.8092 (mt)
REVERT: J   54 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.5877 (pp)
  outliers start: 13
  outliers final: 8
  residues processed: 158
  average time/residue: 0.0735
  time to fit residues: 15.8756
Evaluate side-chains
  150 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 140
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  545 SER
Chi-restraints excluded: chain D residue  596 SER
Chi-restraints excluded: chain D residue  808 MET
Chi-restraints excluded: chain I residue   35 TYR
Chi-restraints excluded: chain I residue   54 LEU
Chi-restraints excluded: chain I residue  110 LEU
Chi-restraints excluded: chain J residue   28 VAL
Chi-restraints excluded: chain J residue   35 TYR
Chi-restraints excluded: chain J residue   54 LEU
Chi-restraints excluded: chain J residue  110 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 39 optimal weight:    0.2980
   chunk 57 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.173526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.143434 restraints weight = 9260.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.147666 restraints weight = 4746.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.150015 restraints weight = 3216.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.151786 restraints weight = 2600.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.152675 restraints weight = 2264.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7057  Z= 0.139
  Angle     :  0.476   7.661   9603  Z= 0.245
  Chirality :  0.038   0.147   1132
  Planarity :  0.003   0.040   1156
  Dihedral  :  3.328  38.018    958
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 19.83 %
    Favored  : 77.86 %
  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:  4.71 (0.28), residues: 874
  helix:  3.92 (0.19), residues: 664
  sheet:  0.00 (0.88), residues: 40
  loop :  0.32 (0.46), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 600 
 TYR   0.009   0.001   TYR I  35 
 PHE   0.023   0.001   PHE B 815 
 TRP   0.005   0.001   TRP I 177 
 HIS   0.004   0.002   HIS J  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 7055)
  covalent geometry    : angle       0.47626 ( 9599)
  SS BOND              : bond        0.00041 (    2)
  SS BOND              : angle       0.23694 (    4)
  hydrogen bonds       : bond        0.03967 (  572)
  hydrogen bonds       : angle       3.21111 ( 1671)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 150
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A  530 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7887 (tp)
REVERT: A  588 SER cc_start: 0.9334 (t) cc_final: 0.8927 (p)
REVERT: B  591 ASP cc_start: 0.7688 (p0) cc_final: 0.7191 (p0)
REVERT: I   22 LEU cc_start: 0.8567 (tp) cc_final: 0.8072 (mt)
REVERT: I   54 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.5926 (pp)
REVERT: J   22 LEU cc_start: 0.8550 (tp) cc_final: 0.8059 (mt)
REVERT: J   54 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.5846 (pp)
  outliers start: 16
  outliers final: 11
  residues processed: 160
  average time/residue: 0.0654
  time to fit residues: 14.3424
Evaluate side-chains
  158 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 144
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  530 ILE
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain D residue  511 SER
Chi-restraints excluded: chain D residue  545 SER
Chi-restraints excluded: chain D residue  596 SER
Chi-restraints excluded: chain D residue  808 MET
Chi-restraints excluded: chain I residue   28 VAL
Chi-restraints excluded: chain I residue   35 TYR
Chi-restraints excluded: chain I residue   54 LEU
Chi-restraints excluded: chain I residue  110 LEU
Chi-restraints excluded: chain J residue   28 VAL
Chi-restraints excluded: chain J residue   35 TYR
Chi-restraints excluded: chain J residue   54 LEU
Chi-restraints excluded: chain J residue  110 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    1.5188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.156320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.124888 restraints weight = 9341.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.128398 restraints weight = 4898.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.130644 restraints weight = 3383.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.131819 restraints weight = 2718.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.132721 restraints weight = 2412.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.2837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   7057  Z= 0.246
  Angle     :  0.571   7.461   9603  Z= 0.302
  Chirality :  0.041   0.156   1132
  Planarity :  0.003   0.038   1156
  Dihedral  :  3.637  38.406    958
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 19.54 %
    Favored  : 77.57 %
  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 (0.28), residues: 874
  helix:  3.46 (0.19), residues: 666
  sheet:  0.73 (0.73), residues: 60
  loop : -0.42 (0.48), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 595 
 TYR   0.013   0.002   TYR J 152 
 PHE   0.019   0.001   PHE D 815 
 TRP   0.005   0.001   TRP A 574 
 HIS   0.007   0.002   HIS I  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00594 ( 7055)
  covalent geometry    : angle       0.57117 ( 9599)
  SS BOND              : bond        0.00067 (    2)
  SS BOND              : angle       0.40584 (    4)
  hydrogen bonds       : bond        0.04948 (  572)
  hydrogen bonds       : angle       3.59173 ( 1671)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 162
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  588 SER cc_start: 0.9377 (t) cc_final: 0.9045 (p)
REVERT: A  595 ARG cc_start: 0.8323 (mtt180) cc_final: 0.7758 (mtt90)
REVERT: B  591 ASP cc_start: 0.7779 (p0) cc_final: 0.7375 (p0)
REVERT: D  595 ARG cc_start: 0.8128 (mtt180) cc_final: 0.7602 (tmt170)
REVERT: I   22 LEU cc_start: 0.8667 (tp) cc_final: 0.8111 (mt)
REVERT: I   54 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.5842 (pp)
REVERT: J   22 LEU cc_start: 0.8623 (tp) cc_final: 0.8065 (mt)
REVERT: J   54 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.5837 (pp)
REVERT: J  189 LYS cc_start: 0.8606 (mttm) cc_final: 0.8403 (mttm)
  outliers start: 20
  outliers final: 13
  residues processed: 174
  average time/residue: 0.0730
  time to fit residues: 16.8291
Evaluate side-chains
  171 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 156
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  512 SER
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  781 SER
Chi-restraints excluded: chain B residue  545 SER
Chi-restraints excluded: chain B residue  629 ARG
Chi-restraints excluded: chain D residue  545 SER
Chi-restraints excluded: chain D residue  596 SER
Chi-restraints excluded: chain D residue  629 ARG
Chi-restraints excluded: chain D residue  808 MET
Chi-restraints excluded: chain I residue   28 VAL
Chi-restraints excluded: chain I residue   35 TYR
Chi-restraints excluded: chain I residue   54 LEU
Chi-restraints excluded: chain J residue   28 VAL
Chi-restraints excluded: chain J residue   35 TYR
Chi-restraints excluded: chain J residue   54 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 75 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 78 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
C 583 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.179628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.147878 restraints weight = 9316.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.152045 restraints weight = 4863.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.154373 restraints weight = 3336.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.156154 restraints weight = 2714.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.157037 restraints weight = 2365.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.2775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7057  Z= 0.137
  Angle     :  0.477   7.188   9603  Z= 0.247
  Chirality :  0.038   0.157   1132
  Planarity :  0.003   0.040   1156
  Dihedral  :  3.414  38.678    958
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 21.13 %
    Favored  : 76.56 %
  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:  4.47 (0.28), residues: 874
  helix:  3.79 (0.19), residues: 664
  sheet:  0.69 (0.72), residues: 60
  loop : -0.37 (0.48), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 600 
 TYR   0.010   0.001   TYR J 152 
 PHE   0.017   0.001   PHE B 815 
 TRP   0.006   0.001   TRP I 177 
 HIS   0.004   0.002   HIS I  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 7055)
  covalent geometry    : angle       0.47665 ( 9599)
  SS BOND              : bond        0.00021 (    2)
  SS BOND              : angle       0.20290 (    4)
  hydrogen bonds       : bond        0.04082 (  572)
  hydrogen bonds       : angle       3.29008 ( 1671)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 150
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  530 ILE cc_start: 0.8118 (mt) cc_final: 0.7868 (tp)
REVERT: A  588 SER cc_start: 0.9347 (t) cc_final: 0.8983 (p)
REVERT: B  591 ASP cc_start: 0.7775 (p0) cc_final: 0.7428 (p0)
REVERT: D  595 ARG cc_start: 0.8094 (mtt180) cc_final: 0.7560 (tmt170)
REVERT: I   22 LEU cc_start: 0.8518 (tp) cc_final: 0.8066 (mt)
REVERT: I   54 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.5973 (pp)
REVERT: J   22 LEU cc_start: 0.8515 (tp) cc_final: 0.8027 (mt)
REVERT: J   54 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.5955 (pp)
  outliers start: 16
  outliers final: 14
  residues processed: 160
  average time/residue: 0.0665
  time to fit residues: 14.7626
Evaluate side-chains
  161 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  512 SER
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  781 SER
Chi-restraints excluded: chain B residue  629 ARG
Chi-restraints excluded: chain D residue  545 SER
Chi-restraints excluded: chain D residue  596 SER
Chi-restraints excluded: chain D residue  629 ARG
Chi-restraints excluded: chain D residue  808 MET
Chi-restraints excluded: chain I residue   28 VAL
Chi-restraints excluded: chain I residue   35 TYR
Chi-restraints excluded: chain I residue   54 LEU
Chi-restraints excluded: chain I residue  110 LEU
Chi-restraints excluded: chain J residue   28 VAL
Chi-restraints excluded: chain J residue   35 TYR
Chi-restraints excluded: chain J residue   54 LEU
Chi-restraints excluded: chain J residue  110 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 8 optimal weight:    0.1980
   chunk 80 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 68 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
C 583 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.180086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.148383 restraints weight = 9269.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.152533 restraints weight = 4875.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.155168 restraints weight = 3357.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.156544 restraints weight = 2684.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.157628 restraints weight = 2376.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.2824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7057  Z= 0.134
  Angle     :  0.490   8.230   9603  Z= 0.249
  Chirality :  0.038   0.169   1132
  Planarity :  0.003   0.040   1156
  Dihedral  :  3.348  38.570    958
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 20.98 %
    Favored  : 76.41 %
  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:  4.60 (0.28), residues: 874
  helix:  3.89 (0.19), residues: 666
  sheet:  0.68 (0.72), residues: 60
  loop : -0.38 (0.49), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 595 
 TYR   0.009   0.001   TYR I  35 
 PHE   0.023   0.001   PHE D 815 
 TRP   0.006   0.001   TRP C 601 
 HIS   0.004   0.002   HIS J  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 7055)
  covalent geometry    : angle       0.49016 ( 9599)
  SS BOND              : bond        0.00025 (    2)
  SS BOND              : angle       0.21443 (    4)
  hydrogen bonds       : bond        0.03960 (  572)
  hydrogen bonds       : angle       3.24943 ( 1671)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 151
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A  530 ILE cc_start: 0.8017 (mt) cc_final: 0.7769 (tp)
REVERT: A  588 SER cc_start: 0.9348 (t) cc_final: 0.8984 (p)
REVERT: B  517 SER cc_start: 0.8290 (t) cc_final: 0.7840 (p)
REVERT: B  591 ASP cc_start: 0.7800 (p0) cc_final: 0.7446 (p0)
REVERT: D  595 ARG cc_start: 0.8195 (mtt180) cc_final: 0.7553 (tmt170)
REVERT: I   54 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.5971 (pp)
REVERT: J   22 LEU cc_start: 0.8480 (tp) cc_final: 0.7992 (mt)
REVERT: J   54 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.5933 (pp)
  outliers start: 18
  outliers final: 14
  residues processed: 162
  average time/residue: 0.0652
  time to fit residues: 14.4523
Evaluate side-chains
  164 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  512 SER
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  781 SER
Chi-restraints excluded: chain B residue  545 SER
Chi-restraints excluded: chain D residue  545 SER
Chi-restraints excluded: chain D residue  596 SER
Chi-restraints excluded: chain D residue  629 ARG
Chi-restraints excluded: chain D residue  808 MET
Chi-restraints excluded: chain I residue   28 VAL
Chi-restraints excluded: chain I residue   35 TYR
Chi-restraints excluded: chain I residue   54 LEU
Chi-restraints excluded: chain I residue  110 LEU
Chi-restraints excluded: chain J residue   28 VAL
Chi-restraints excluded: chain J residue   35 TYR
Chi-restraints excluded: chain J residue   54 LEU
Chi-restraints excluded: chain J residue  110 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 46 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0070
   chunk 30 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   chunk 77 optimal weight:    0.3980
   chunk 60 optimal weight:    0.1980
   overall best weight:    0.3798

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

Flipped N/Q/H residues before XYZ refinement:
C 583 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.176117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.145424 restraints weight = 9179.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.149688 restraints weight = 4756.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.152354 restraints weight = 3232.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.153492 restraints weight = 2574.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.154792 restraints weight = 2300.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7057  Z= 0.111
  Angle     :  0.460   6.617   9603  Z= 0.235
  Chirality :  0.037   0.196   1132
  Planarity :  0.003   0.040   1156
  Dihedral  :  3.236  38.234    958
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 21.42 %
    Favored  : 76.70 %
  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:  4.91 (0.29), residues: 874
  helix:  4.22 (0.19), residues: 654
  sheet:  0.69 (0.72), residues: 60
  loop : -0.34 (0.48), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 590 
 TYR   0.008   0.001   TYR D 534 
 PHE   0.020   0.001   PHE B 815 
 TRP   0.007   0.001   TRP J 177 
 HIS   0.004   0.002   HIS J 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 7055)
  covalent geometry    : angle       0.46016 ( 9599)
  SS BOND              : bond        0.00024 (    2)
  SS BOND              : angle       0.17919 (    4)
  hydrogen bonds       : bond        0.03552 (  572)
  hydrogen bonds       : angle       3.10623 ( 1671)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 155
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  588 SER cc_start: 0.9320 (t) cc_final: 0.8979 (p)
REVERT: B  591 ASP cc_start: 0.7763 (p0) cc_final: 0.7410 (p0)
REVERT: C  530 ILE cc_start: 0.8449 (mt) cc_final: 0.8211 (tp)
REVERT: C  540 SER cc_start: 0.8406 (m) cc_final: 0.7928 (p)
REVERT: D  595 ARG cc_start: 0.8171 (mtt180) cc_final: 0.7664 (tmt170)
REVERT: I   54 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.5967 (pt)
REVERT: J   22 LEU cc_start: 0.8456 (tp) cc_final: 0.7971 (mt)
  outliers start: 13
  outliers final: 12
  residues processed: 162
  average time/residue: 0.0640
  time to fit residues: 14.1856
Evaluate side-chains
  163 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 150
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  512 SER
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain B residue  545 SER
Chi-restraints excluded: chain C residue  512 SER
Chi-restraints excluded: chain D residue  545 SER
Chi-restraints excluded: chain D residue  596 SER
Chi-restraints excluded: chain D residue  629 ARG
Chi-restraints excluded: chain D residue  808 MET
Chi-restraints excluded: chain I residue   35 TYR
Chi-restraints excluded: chain I residue   54 LEU
Chi-restraints excluded: chain J residue   35 TYR
Chi-restraints excluded: chain J residue   54 LEU
Chi-restraints excluded: chain J residue  110 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 55 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0570
   chunk 24 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
C 583 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.173431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.142557 restraints weight = 9212.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.146721 restraints weight = 4824.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.149219 restraints weight = 3306.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.150949 restraints weight = 2662.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.151810 restraints weight = 2316.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.2916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7057  Z= 0.141
  Angle     :  0.502   8.667   9603  Z= 0.256
  Chirality :  0.039   0.190   1132
  Planarity :  0.003   0.040   1156
  Dihedral  :  3.267  38.191    958
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 21.27 %
    Favored  : 76.41 %
  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:  4.74 (0.28), residues: 874
  helix:  4.08 (0.19), residues: 654
  sheet:  0.71 (0.72), residues: 60
  loop : -0.38 (0.48), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 595 
 TYR   0.009   0.001   TYR I  35 
 PHE   0.024   0.001   PHE D 815 
 TRP   0.006   0.001   TRP C 601 
 HIS   0.004   0.002   HIS J  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 7055)
  covalent geometry    : angle       0.50221 ( 9599)
  SS BOND              : bond        0.00001 (    2)
  SS BOND              : angle       0.17310 (    4)
  hydrogen bonds       : bond        0.03910 (  572)
  hydrogen bonds       : angle       3.25314 ( 1671)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1159.57 seconds
wall clock time: 20 minutes 40.56 seconds (1240.56 seconds total)