Starting phenix.real_space_refine
on Fri Feb 14 20:25:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j6m_36008/02_2025/8j6m_36008.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j6m_36008/02_2025/8j6m_36008.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j6m_36008/02_2025/8j6m_36008.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j6m_36008/02_2025/8j6m_36008.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j6m_36008/02_2025/8j6m_36008.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j6m_36008/02_2025/8j6m_36008.cif"
  }
  resolution = 2.77
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.153
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      56      5.16       5
     Na      1      4.78       5
     C    7084      2.51       5
     N    1644      2.21       5
     O    1812      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 62 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10599
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 5165
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 641, 5156
          Classifications: {'peptide': 641}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 616}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 22
      Conformer: "B"
        Number of residues, atoms: 641, 5156
          Classifications: {'peptide': 641}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 616}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 22
          bond proxies already assigned to first conformer: 5284
    Chain: "A"
      Number of atoms: 5165
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 641, 5156
          Classifications: {'peptide': 641}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 616}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 22
      Conformer: "B"
        Number of residues, atoms: 641, 5156
          Classifications: {'peptide': 641}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 616}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 22
          bond proxies already assigned to first conformer: 5284
    Chain: "B"
      Number of atoms: 134
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 134
          Unusual residues: {' NA': 1, ' ZN': 1, 'CLR': 4, 'OLA': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
    Chain: "A"
      Number of atoms: 133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 133
          Unusual residues: {' ZN': 1, 'CLR': 4, 'OLA': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 11.10, per 1000 atoms: 1.05
  Number of scatterers: 10599
  At special positions: 0
  Unit cell: (113.36, 86.32, 126.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      56     16.00
     Na      1     11.00
     O    1812      8.00
     N    1644      7.00
     C    7084      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 130 " - pdb=" SG  CYS B 222 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 212 " - pdb=" SG  CYS B 271 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 479 " - pdb=" SG  CYS B 565 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 485 " - pdb=" SG  CYS B 782 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 130 " - pdb=" SG  CYS A 222 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 212 " - pdb=" SG  CYS A 271 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 479 " - pdb=" SG  CYS A 565 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 485 " - pdb=" SG  CYS A 782 " distance=2.07

  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: 2.78
  Conformation dependent library (CDL) restraints added in 2.7 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 901 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 791 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 795 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 563 "
      pdb="  ZN B 905 "
        pdb="ZN    ZN B 905 " - pdb=" NE2 HIS B 795 "
        pdb="ZN    ZN B 905 " - pdb=" NE2 HIS B 563 "
        pdb="ZN    ZN B 905 " - pdb=" NE2 HIS B 791 "


  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2464

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 10 sheets defined
      50.5% alpha, 17.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.45
  Creating SS restraints...
    Processing helix  chain 'B' and resid 251 through 255
      Proline residue:  B 254  - end of helix
      No H-bonds generated for 'chain 'B' and resid 251 through 255'
    Processing helix  chain 'B' and resid 302 through 338
      removed outlier: 3.833A  pdb=" N   TYR B 306 " --> pdb=" O   LYS B 302 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   PHE B 317 " --> pdb=" O   SER B 313 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   PHE B 320 " --> pdb=" O   ILE B 316 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   TYR B 321 " --> pdb=" O   PHE B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 474
      removed outlier: 4.509A  pdb=" N   TRP B 446 " --> pdb=" O   LYS B 442 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ILE B 449 " --> pdb=" O   PHE B 445 " (cutoff:3.500A)
      Proline residue:  B 458  - end of helix
      removed outlier: 3.605A  pdb=" N   THR B 465 " --> pdb=" O   GLN B 461 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 486
      removed outlier: 3.727A  pdb=" N   ALA B 486 " --> pdb=" O   PHE B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 494 through 500
      removed outlier: 3.934A  pdb=" N   ILE B 498 " --> pdb=" O   ALA B 494 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 501 through 528
      removed outlier: 3.891A  pdb=" N   VAL B 505 " --> pdb=" O   ASN B 501 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 530 through 536
    Processing helix  chain 'B' and resid 542 through 563
    Processing helix  chain 'B' and resid 570 through 575
      removed outlier: 3.808A  pdb=" N   ASP B 574 " --> pdb=" O   PHE B 571 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 576 through 594
      removed outlier: 3.851A  pdb=" N   MET B 580 " --> pdb=" O   SER B 576 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ARG B 593 " --> pdb=" O   LEU B 589 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 600 through 622
      removed outlier: 3.555A  pdb=" N   ALA B 604 " --> pdb=" O   SER B 600 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 625 through 648
      removed outlier: 3.583A  pdb=" N   THR B 645 " --> pdb=" O   LEU B 641 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLN B 646 " --> pdb=" O   ALA B 642 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 683 through 705
      removed outlier: 3.970A  pdb=" N   ASN B 694 " --> pdb=" O   GLY B 690 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 708 through 735
    Processing helix  chain 'B' and resid 740 through 762
    Processing helix  chain 'B' and resid 771 through 777
      removed outlier: 3.514A  pdb=" N   GLU B 777 " --> pdb=" O   ALA B 773 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 789 through 812
      removed outlier: 3.537A  pdb=" N   ALA B 799 " --> pdb=" O   HIS B 795 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 813 through 818
      removed outlier: 3.693A  pdb=" N   ASP B 817 " --> pdb=" O   ASP B 814 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   VAL B 818 " --> pdb=" O   ASP B 815 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 255
      Proline residue:  A 254  - end of helix
      No H-bonds generated for 'chain 'A' and resid 251 through 255'
    Processing helix  chain 'A' and resid 302 through 338
      removed outlier: 3.834A  pdb=" N   TYR A 306 " --> pdb=" O   LYS A 302 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   PHE A 317 " --> pdb=" O   SER A 313 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   PHE A 320 " --> pdb=" O   ILE A 316 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   TYR A 321 " --> pdb=" O   PHE A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 474
      removed outlier: 4.504A  pdb=" N   TRP A 446 " --> pdb=" O   LYS A 442 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ILE A 449 " --> pdb=" O   PHE A 445 " (cutoff:3.500A)
      Proline residue:  A 458  - end of helix
      removed outlier: 3.603A  pdb=" N   THR A 465 " --> pdb=" O   GLN A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 500
      removed outlier: 3.909A  pdb=" N   ILE A 498 " --> pdb=" O   ALA A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 529
      removed outlier: 3.777A  pdb=" N   VAL A 505 " --> pdb=" O   ASN A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 536
    Processing helix  chain 'A' and resid 542 through 565
      removed outlier: 4.139A  pdb=" N   CYS A 565 " --> pdb=" O   CYS A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 594
      removed outlier: 3.803A  pdb=" N   MET A 580 " --> pdb=" O   SER A 576 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ARG A 593 " --> pdb=" O   LEU A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 622
      removed outlier: 3.553A  pdb=" N   ALA A 604 " --> pdb=" O   SER A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 625 through 648
    Processing helix  chain 'A' and resid 683 through 705
      removed outlier: 3.503A  pdb=" N   ASN A 694 " --> pdb=" O   GLY A 690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 735
    Processing helix  chain 'A' and resid 740 through 762
    Processing helix  chain 'A' and resid 771 through 777
      removed outlier: 3.568A  pdb=" N   GLU A 777 " --> pdb=" O   ALA A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 789 through 812
      removed outlier: 3.537A  pdb=" N   ALA A 799 " --> pdb=" O   HIS A 795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 813 through 819
      removed outlier: 3.502A  pdb=" N   ASP A 817 " --> pdb=" O   ASP A 814 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   VAL A 818 " --> pdb=" O   ASP A 815 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 50 through 56
      removed outlier: 4.390A  pdb=" N   HIS B  50 " --> pdb=" O   VAL B 163 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   VAL B 163 " --> pdb=" O   HIS B  50 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   ALA B  77 " --> pdb=" O   LEU B 166 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   VAL B  78 " --> pdb=" O   LEU B 129 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 62 through 70
    Processing sheet with id=AA3, first strand: chain 'B' and resid 110 through 114
    Processing sheet with id=AA4, first strand: chain 'B' and resid 170 through 171
      removed outlier: 4.793A  pdb=" N   LYS B 192 " --> pdb=" O   LEU B 171 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 176 through 181
    Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 56
      removed outlier: 4.390A  pdb=" N   HIS A  50 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   VAL A 163 " --> pdb=" O   HIS A  50 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   ALA A  77 " --> pdb=" O   LEU A 166 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   VAL A  78 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 62 through 70
    Processing sheet with id=AA8, first strand: chain 'A' and resid 110 through 114
    Processing sheet with id=AA9, first strand: chain 'A' and resid 170 through 171
      removed outlier: 4.794A  pdb=" N   LYS A 192 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 176 through 181

    634 hydrogen bonds defined for protein.
    1822 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: 3.44

  Time building geometry restraints manager: 3.15 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1967
        1.32 -     1.45: 3197
        1.45 -     1.59: 5648
        1.59 -     1.72: 0
        1.72 -     1.85: 86
  Bond restraints: 10898
  Sorted by residual:
  bond pdb=" C   TYR A  81 "
       pdb=" CA BTYR A  81 "
    ideal  model  delta    sigma   weight residual
    1.521  1.422  0.099 1.19e-02 7.06e+03 6.96e+01
  bond pdb=" C10 OLA A 906 "
       pdb=" C9  OLA A 906 "
    ideal  model  delta    sigma   weight residual
    1.332  1.470 -0.138 2.00e-02 2.50e+03 4.73e+01
  bond pdb=" C10 OLA B 907 "
       pdb=" C9  OLA B 907 "
    ideal  model  delta    sigma   weight residual
    1.332  1.469 -0.137 2.00e-02 2.50e+03 4.72e+01
  bond pdb=" N   TYR B  81 "
       pdb=" CA BTYR B  81 "
    ideal  model  delta    sigma   weight residual
    1.456  1.409  0.048 1.21e-02 6.83e+03 1.55e+01
  bond pdb=" CA  VAL A 108 "
       pdb=" C   VAL A 108 "
    ideal  model  delta    sigma   weight residual
    1.525  1.557 -0.033 9.10e-03 1.21e+04 1.29e+01
  ... (remaining 10893 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 14191
        2.39 -     4.79: 547
        4.79 -     7.18: 96
        7.18 -     9.58: 28
        9.58 -    11.97: 6
  Bond angle restraints: 14868
  Sorted by residual:
  angle pdb=" N   VAL A 534 "
        pdb=" CA  VAL A 534 "
        pdb=" C   VAL A 534 "
      ideal   model   delta    sigma   weight residual
     110.53  119.47   -8.94 9.40e-01 1.13e+00 9.04e+01
  angle pdb=" N   SER A 274 "
        pdb=" CA  SER A 274 "
        pdb=" C   SER A 274 "
      ideal   model   delta    sigma   weight residual
     111.28  121.07   -9.79 1.09e+00 8.42e-01 8.06e+01
  angle pdb=" N   VAL B 534 "
        pdb=" CA  VAL B 534 "
        pdb=" C   VAL B 534 "
      ideal   model   delta    sigma   weight residual
     110.53  118.91   -8.38 9.40e-01 1.13e+00 7.95e+01
  angle pdb=" N   PHE B 275 "
        pdb=" CA  PHE B 275 "
        pdb=" C   PHE B 275 "
      ideal   model   delta    sigma   weight residual
     110.19  119.77   -9.58 1.24e+00 6.50e-01 5.97e+01
  angle pdb=" N   LEU A 155 "
        pdb=" CA  LEU A 155 "
        pdb=" C   LEU A 155 "
      ideal   model   delta    sigma   weight residual
     110.17   98.20   11.97 1.61e+00 3.86e-01 5.53e+01
  ... (remaining 14863 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.91: 6274
       24.91 -    49.82: 410
       49.82 -    74.73: 46
       74.73 -    99.64: 17
       99.64 -   124.55: 3
  Dihedral angle restraints: 6750
    sinusoidal: 2932
      harmonic: 3818
  Sorted by residual:
  dihedral pdb=" CB  CYS A 485 "
           pdb=" SG  CYS A 485 "
           pdb=" SG  CYS A 782 "
           pdb=" CB  CYS A 782 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   34.75   58.25     1      1.00e+01 1.00e-02 4.55e+01
  dihedral pdb=" CB  CYS B 485 "
           pdb=" SG  CYS B 485 "
           pdb=" SG  CYS B 782 "
           pdb=" CB  CYS B 782 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.35   55.65     1      1.00e+01 1.00e-02 4.18e+01
  dihedral pdb=" CA  CYS A 782 "
           pdb=" C   CYS A 782 "
           pdb=" N   ILE A 783 "
           pdb=" CA  ILE A 783 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.73  -25.27     0      5.00e+00 4.00e-02 2.55e+01
  ... (remaining 6747 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.101: 1445
       0.101 -    0.202: 196
       0.202 -    0.303: 52
       0.303 -    0.404: 12
       0.404 -    0.506: 5
  Chirality restraints: 1710
  Sorted by residual:
  chirality pdb=" CA  PHE B 317 "
            pdb=" N   PHE B 317 "
            pdb=" C   PHE B 317 "
            pdb=" CB  PHE B 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.39e+00
  chirality pdb=" CA  PHE A 317 "
            pdb=" N   PHE A 317 "
            pdb=" C   PHE A 317 "
            pdb=" CB  PHE A 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.51 2.00e-01 2.50e+01 6.38e+00
  chirality pdb=" CA  ASN B  83 "
            pdb=" N   ASN B  83 "
            pdb=" C   ASN B  83 "
            pdb=" CB  ASN B  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.29e+00
  ... (remaining 1707 not shown)

  Planarity restraints: 1806
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 OLA A 906 "   -0.279 2.00e-02 2.50e+03   2.13e-01 4.54e+02
        pdb=" C11 OLA A 906 "    0.114 2.00e-02 2.50e+03
        pdb=" C8  OLA A 906 "   -0.115 2.00e-02 2.50e+03
        pdb=" C9  OLA A 906 "    0.279 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 OLA B 907 "    0.279 2.00e-02 2.50e+03   2.13e-01 4.54e+02
        pdb=" C11 OLA B 907 "   -0.114 2.00e-02 2.50e+03
        pdb=" C8  OLA B 907 "    0.114 2.00e-02 2.50e+03
        pdb=" C9  OLA B 907 "   -0.279 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 525 "    0.017 2.00e-02 2.50e+03   3.48e-02 1.21e+01
        pdb=" C   ALA B 525 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   ALA B 525 "    0.023 2.00e-02 2.50e+03
        pdb=" N   LEU B 526 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1803 not shown)

  Histogram of nonbonded interaction distances:
        1.86 -     2.47: 28
        2.47 -     3.07: 7058
        3.07 -     3.68: 15994
        3.68 -     4.29: 26004
        4.29 -     4.90: 42374
  Nonbonded interactions: 91458
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 574 "
            pdb="ZN    ZN B 905 "
     model   vdw
     1.857 2.230
  nonbonded pdb=" NE2 GLN B 100 "
            pdb=" O   ASN A  90 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" OD1 ASP A 574 "
            pdb="ZN    ZN A 901 "
     model   vdw
     2.292 2.230
  nonbonded pdb=" NZ  LYS B 732 "
            pdb=" OD1 ASP B 813 "
     model   vdw
     2.302 3.120
  nonbonded pdb=" NZ  LYS A 732 "
            pdb=" OD1 ASP A 813 "
     model   vdw
     2.302 3.120
  ... (remaining 91453 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 44 through 80 or resid 82 through 827 or resid 902 through \ 
 904))
  selection = (chain 'B' and (resid 44 through 80 or resid 82 through 827 or resid 902 through \ 
 904))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.310
  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:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.080
  Process input model:                     35.040
  Find NCS groups from input model:        0.490
  Set up NCS constraints:                  0.060
  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:13.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
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      :  0.008   0.138  10898  Z= 0.522
  Angle     :  1.104  11.972  14868  Z= 0.699
  Chirality :  0.083   0.506   1710
  Planarity :  0.009   0.213   1806
  Dihedral  : 16.073 124.552   4262
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.29 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 16.96 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.41 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.22), residues: 1268
  helix:  1.31 (0.20), residues: 580
  sheet:  1.50 (0.27), residues: 284
  loop : -0.95 (0.28), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 106 
 HIS   0.004   0.001   HIS A 636 
 PHE   0.023   0.002   PHE A 317 
 TYR   0.021   0.002   TYR B 605 
 ARG   0.007   0.001   ARG A 289 

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

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

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 189
  time to evaluate  : 1.115 
Fit side-chains
REVERT: B   61 GLU cc_start: 0.8596 (tt0) cc_final: 0.8376 (tt0)
REVERT: B  118 ARG cc_start: 0.7270 (ttm-80) cc_final: 0.6760 (mtp180)
REVERT: B  123 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8288 (mm110)
REVERT: B  302 LYS cc_start: 0.7700 (mmtt) cc_final: 0.7401 (mmtt)
REVERT: B  586 MET cc_start: 0.8307 (mtm) cc_final: 0.8098 (mtp)
REVERT: B  684 MET cc_start: 0.5846 (tmt) cc_final: 0.5295 (mpp)
REVERT: B  702 LEU cc_start: 0.7717 (tp) cc_final: 0.7302 (tt)
REVERT: B  707 ARG cc_start: 0.7243 (tpp80) cc_final: 0.6898 (mmm160)
REVERT: B  738 LYS cc_start: 0.7521 (mttt) cc_final: 0.7302 (mtpm)
REVERT: A   61 GLU cc_start: 0.8588 (tt0) cc_final: 0.8357 (tt0)
REVERT: A  118 ARG cc_start: 0.7207 (ttm-80) cc_final: 0.6685 (mtp180)
REVERT: A  302 LYS cc_start: 0.8036 (mptm) cc_final: 0.7561 (mmtt)
REVERT: A  505 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.8235 (m)
REVERT: A  684 MET cc_start: 0.5580 (tmt) cc_final: 0.5113 (mpp)
REVERT: A  707 ARG cc_start: 0.7280 (tpp80) cc_final: 0.6963 (mmm160)
REVERT: A  774 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7634 (mt-10)
  outliers start: 18
  outliers final: 9
  residues processed: 203
  average time/residue: 1.0568
  time to fit residues: 234.3198
Evaluate side-chains
  168 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 158
  time to evaluate  : 1.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  596 ASP
Chi-restraints excluded: chain B residue  764 ASN
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  596 ASP
Chi-restraints excluded: chain A residue  764 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 116 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 461 GLN
B 720 ASN
A 461 GLN
A 475 ASN
A 541 HIS
A 646 GLN
A 694 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.153535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.120311 restraints weight = 20601.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 3.10
r_work: 0.3089 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3079
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3079
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.1484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  10898  Z= 0.255
  Angle     :  0.606   7.245  14868  Z= 0.310
  Chirality :  0.045   0.190   1710
  Planarity :  0.004   0.035   1806
  Dihedral  :  8.469  55.936   1964
  Min Nonbonded Distance : 1.784

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 18.29 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.22), residues: 1268
  helix:  2.23 (0.19), residues: 584
  sheet:  1.33 (0.28), residues: 284
  loop : -0.83 (0.28), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 629 
 HIS   0.005   0.001   HIS B 563 
 PHE   0.023   0.002   PHE A 317 
 TYR   0.015   0.002   TYR A 605 
 ARG   0.006   0.001   ARG A 593 

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

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

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 171
  time to evaluate  : 1.239 
Fit side-chains
REVERT: B   61 GLU cc_start: 0.8297 (tt0) cc_final: 0.8057 (tt0)
REVERT: B   90 ASN cc_start: 0.7839 (m-40) cc_final: 0.7622 (m-40)
REVERT: B  118 ARG cc_start: 0.7320 (ttm-80) cc_final: 0.6689 (mtp180)
REVERT: B  158 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7836 (mt0)
REVERT: B  274 SER cc_start: 0.7439 (m) cc_final: 0.7197 (t)
REVERT: B  536 TYR cc_start: 0.7351 (m-80) cc_final: 0.7135 (m-80)
REVERT: B  576 SER cc_start: 0.8317 (m) cc_final: 0.7993 (p)
REVERT: B  684 MET cc_start: 0.5726 (tmt) cc_final: 0.4975 (mpm)
REVERT: B  702 LEU cc_start: 0.7552 (tp) cc_final: 0.7187 (tt)
REVERT: B  707 ARG cc_start: 0.7177 (tpp80) cc_final: 0.6770 (mmm160)
REVERT: B  738 LYS cc_start: 0.7610 (mttt) cc_final: 0.7162 (mtpm)
REVERT: A  118 ARG cc_start: 0.7403 (ttm-80) cc_final: 0.6547 (mtp180)
REVERT: A  158 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7804 (mt0)
REVERT: A  302 LYS cc_start: 0.7891 (mptm) cc_final: 0.7596 (mmtm)
REVERT: A  536 TYR cc_start: 0.7460 (m-80) cc_final: 0.7150 (m-80)
REVERT: A  576 SER cc_start: 0.8294 (m) cc_final: 0.7987 (p)
REVERT: A  684 MET cc_start: 0.5486 (tmt) cc_final: 0.4836 (mpp)
REVERT: A  692 LEU cc_start: 0.7189 (mp) cc_final: 0.6954 (mp)
REVERT: A  707 ARG cc_start: 0.7182 (tpp80) cc_final: 0.6730 (mmm160)
REVERT: A  738 LYS cc_start: 0.6913 (mtpm) cc_final: 0.5703 (mmtp)
REVERT: A  774 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7743 (mt-10)
  outliers start: 34
  outliers final: 18
  residues processed: 192
  average time/residue: 0.9577
  time to fit residues: 202.6493
Evaluate side-chains
  179 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 159
  time to evaluate  : 1.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  102 GLU
Chi-restraints excluded: chain B residue  158 GLN
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  596 ASP
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  158 GLN
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  596 ASP
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  713 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 81 optimal weight:    0.0870
   chunk 14 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 122 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 100 optimal weight:    2.9990
   chunk 118 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   overall best weight:    1.1160

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

Flipped N/Q/H residues before XYZ refinement:
B 123 GLN
B 475 ASN
B 720 ASN
B 779 ASN
A 646 GLN
A 764 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.151785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.118466 restraints weight = 18976.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 2.87
r_work: 0.3088 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2917
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2917 r_free = 0.2917    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2917 r_free = 0.2917    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2917
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.1735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  10898  Z= 0.284
  Angle     :  0.570   7.501  14868  Z= 0.294
  Chirality :  0.044   0.145   1710
  Planarity :  0.004   0.037   1806
  Dihedral  :  7.394  57.208   1956
  Min Nonbonded Distance : 1.809

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 18.99 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.22), residues: 1268
  helix:  2.37 (0.20), residues: 584
  sheet:  1.15 (0.29), residues: 284
  loop : -0.81 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 106 
 HIS   0.005   0.001   HIS A 563 
 PHE   0.016   0.002   PHE A 317 
 TYR   0.021   0.002   TYR A 605 
 ARG   0.005   0.001   ARG A 172 

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

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

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 165
  time to evaluate  : 1.506 
Fit side-chains
REVERT: B  118 ARG cc_start: 0.7354 (ttm-80) cc_final: 0.6629 (mtp180)
REVERT: B  172 ARG cc_start: 0.8300 (mpt180) cc_final: 0.8053 (mmt-90)
REVERT: B  207 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7198 (mp0)
REVERT: B  274 SER cc_start: 0.7354 (OUTLIER) cc_final: 0.7105 (t)
REVERT: B  297 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8506 (mm)
REVERT: B  576 SER cc_start: 0.8548 (m) cc_final: 0.8166 (p)
REVERT: B  684 MET cc_start: 0.5680 (tmt) cc_final: 0.5225 (mpp)
REVERT: B  702 LEU cc_start: 0.7676 (tp) cc_final: 0.7332 (tt)
REVERT: B  707 ARG cc_start: 0.7328 (tpp80) cc_final: 0.6922 (mmm160)
REVERT: B  738 LYS cc_start: 0.7823 (mttt) cc_final: 0.7380 (mtmm)
REVERT: B  753 MET cc_start: 0.8788 (mmt) cc_final: 0.8118 (mmt)
REVERT: A  118 ARG cc_start: 0.7397 (ttm-80) cc_final: 0.6510 (mtp180)
REVERT: A  158 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8353 (mt0)
REVERT: A  207 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7248 (mp0)
REVERT: A  297 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8433 (mm)
REVERT: A  302 LYS cc_start: 0.7918 (mptm) cc_final: 0.7626 (mmmm)
REVERT: A  536 TYR cc_start: 0.7530 (m-80) cc_final: 0.7234 (m-80)
REVERT: A  576 SER cc_start: 0.8477 (m) cc_final: 0.8110 (p)
REVERT: A  684 MET cc_start: 0.5586 (tmt) cc_final: 0.5083 (mpm)
REVERT: A  692 LEU cc_start: 0.7381 (mp) cc_final: 0.7156 (mp)
REVERT: A  707 ARG cc_start: 0.7341 (tpp80) cc_final: 0.6908 (mmm160)
REVERT: A  738 LYS cc_start: 0.7130 (mtpm) cc_final: 0.6266 (mtmm)
REVERT: A  774 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7948 (mt-10)
  outliers start: 38
  outliers final: 22
  residues processed: 188
  average time/residue: 0.9598
  time to fit residues: 200.4641
Evaluate side-chains
  188 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 160
  time to evaluate  : 1.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  102 GLU
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  207 GLU
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  596 ASP
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  158 GLN
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  196 ASP
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  587 LEU
Chi-restraints excluded: chain A residue  596 ASP
Chi-restraints excluded: chain A residue  719 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 115 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 70 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9980
   chunk 21 optimal weight:    0.4980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 646 GLN
B 720 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.152957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.120792 restraints weight = 22838.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 3.39
r_work: 0.3036 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3034
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3034
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10898  Z= 0.225
  Angle     :  0.517   7.159  14868  Z= 0.267
  Chirality :  0.042   0.143   1710
  Planarity :  0.003   0.037   1806
  Dihedral  :  7.161  59.204   1956
  Min Nonbonded Distance : 1.828

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 19.08 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.23), residues: 1268
  helix:  2.54 (0.20), residues: 584
  sheet:  1.11 (0.29), residues: 284
  loop : -0.75 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 106 
 HIS   0.004   0.001   HIS A 487 
 PHE   0.013   0.001   PHE A 317 
 TYR   0.023   0.002   TYR A 605 
 ARG   0.004   0.000   ARG A 172 

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

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

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 164
  time to evaluate  : 1.181 
Fit side-chains
REVERT: B  118 ARG cc_start: 0.7228 (ttm-80) cc_final: 0.6506 (mtp180)
REVERT: B  158 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8148 (mt0)
REVERT: B  207 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7116 (mp0)
REVERT: B  274 SER cc_start: 0.7266 (OUTLIER) cc_final: 0.7060 (t)
REVERT: B  297 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8476 (mm)
REVERT: B  576 SER cc_start: 0.8439 (m) cc_final: 0.8072 (p)
REVERT: B  684 MET cc_start: 0.5522 (tmt) cc_final: 0.5099 (mpm)
REVERT: B  702 LEU cc_start: 0.7588 (tp) cc_final: 0.7269 (tt)
REVERT: B  707 ARG cc_start: 0.7259 (tpp80) cc_final: 0.6792 (mmm160)
REVERT: B  738 LYS cc_start: 0.7524 (mttt) cc_final: 0.7002 (mtmm)
REVERT: B  753 MET cc_start: 0.8631 (mmt) cc_final: 0.7977 (mmt)
REVERT: A   83 ASN cc_start: 0.8281 (p0) cc_final: 0.7994 (p0)
REVERT: A  118 ARG cc_start: 0.7239 (ttm-80) cc_final: 0.6355 (mtp180)
REVERT: A  207 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7168 (mp0)
REVERT: A  297 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8361 (mm)
REVERT: A  524 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6362 (mtt180)
REVERT: A  536 TYR cc_start: 0.7563 (m-80) cc_final: 0.7297 (m-80)
REVERT: A  576 SER cc_start: 0.8545 (m) cc_final: 0.8143 (p)
REVERT: A  684 MET cc_start: 0.5433 (tmt) cc_final: 0.4993 (mpm)
REVERT: A  692 LEU cc_start: 0.7166 (mp) cc_final: 0.6921 (mm)
REVERT: A  707 ARG cc_start: 0.7264 (tpp80) cc_final: 0.6802 (mmm160)
REVERT: A  713 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.8060 (mmm)
REVERT: A  738 LYS cc_start: 0.7006 (mtpm) cc_final: 0.6146 (mtmm)
REVERT: A  774 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7711 (mt-10)
  outliers start: 38
  outliers final: 20
  residues processed: 185
  average time/residue: 0.9884
  time to fit residues: 200.9970
Evaluate side-chains
  180 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 152
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  102 GLU
Chi-restraints excluded: chain B residue  158 GLN
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain B residue  207 GLU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  239 SER
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  463 VAL
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  196 ASP
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  524 ARG
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain A residue  719 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 114 optimal weight:    2.9990
   chunk 117 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 85 optimal weight:    0.5980
   chunk 103 optimal weight:    4.9990
   chunk 92 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 96 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
B 178 HIS
B 646 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.150937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.116671 restraints weight = 17729.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 2.47
r_work: 0.3101 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2938
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2938 r_free = 0.2938    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2938 r_free = 0.2938    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2938
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.2019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  10898  Z= 0.307
  Angle     :  0.564   8.387  14868  Z= 0.289
  Chirality :  0.044   0.144   1710
  Planarity :  0.004   0.037   1806
  Dihedral  :  7.207  59.970   1952
  Min Nonbonded Distance : 1.813

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 19.35 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.23), residues: 1268
  helix:  2.44 (0.20), residues: 584
  sheet:  1.17 (0.30), residues: 272
  loop : -0.87 (0.28), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 629 
 HIS   0.005   0.001   HIS A 563 
 PHE   0.012   0.002   PHE B 632 
 TYR   0.028   0.002   TYR A 605 
 ARG   0.006   0.001   ARG B 172 

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

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

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 153
  time to evaluate  : 1.138 
Fit side-chains
REVERT: B  118 ARG cc_start: 0.7307 (ttm-80) cc_final: 0.6511 (mtp180)
REVERT: B  158 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8227 (mt0)
REVERT: B  207 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7222 (mp0)
REVERT: B  274 SER cc_start: 0.7230 (OUTLIER) cc_final: 0.7011 (t)
REVERT: B  297 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8467 (mm)
REVERT: B  519 ASP cc_start: 0.7114 (t0) cc_final: 0.6784 (t70)
REVERT: B  576 SER cc_start: 0.8466 (m) cc_final: 0.8040 (p)
REVERT: B  684 MET cc_start: 0.5668 (tmt) cc_final: 0.5205 (mpm)
REVERT: B  707 ARG cc_start: 0.7333 (tpp80) cc_final: 0.6817 (mmm160)
REVERT: B  738 LYS cc_start: 0.7568 (mttt) cc_final: 0.7040 (mtmm)
REVERT: A  118 ARG cc_start: 0.7322 (ttm-80) cc_final: 0.6391 (mtp180)
REVERT: A  158 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8232 (mt0)
REVERT: A  207 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7208 (mp0)
REVERT: A  297 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8490 (mm)
REVERT: A  524 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.6447 (mtt180)
REVERT: A  536 TYR cc_start: 0.7619 (m-80) cc_final: 0.7381 (m-80)
REVERT: A  576 SER cc_start: 0.8461 (m) cc_final: 0.8030 (p)
REVERT: A  684 MET cc_start: 0.5567 (tmt) cc_final: 0.5043 (mpm)
REVERT: A  692 LEU cc_start: 0.7182 (mp) cc_final: 0.6890 (mm)
REVERT: A  707 ARG cc_start: 0.7352 (tpp80) cc_final: 0.6820 (mmm160)
REVERT: A  713 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.8093 (mmm)
REVERT: A  774 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7866 (mt-10)
  outliers start: 46
  outliers final: 28
  residues processed: 180
  average time/residue: 0.9695
  time to fit residues: 191.8761
Evaluate side-chains
  186 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 149
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  102 GLU
Chi-restraints excluded: chain B residue  158 GLN
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  207 GLU
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  239 SER
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  463 VAL
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  596 ASP
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  158 GLN
Chi-restraints excluded: chain A residue  196 ASP
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  524 ARG
Chi-restraints excluded: chain A residue  587 LEU
Chi-restraints excluded: chain A residue  596 ASP
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain A residue  719 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 17 optimal weight:    0.0770
   chunk 23 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 126 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 107 optimal weight:    2.9990
   chunk 118 optimal weight:    2.9990
   chunk 127 optimal weight:    0.4980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
B 646 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.153123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.119673 restraints weight = 14152.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 1.92
r_work: 0.3159 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3022 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3009
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3009 r_free = 0.3009    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3009 r_free = 0.3009    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3009
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10898  Z= 0.197
  Angle     :  0.499   7.030  14868  Z= 0.257
  Chirality :  0.041   0.141   1710
  Planarity :  0.003   0.038   1806
  Dihedral  :  6.995  59.216   1952
  Min Nonbonded Distance : 1.838

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 19.79 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.89 (0.23), residues: 1268
  helix:  2.64 (0.20), residues: 584
  sheet:  1.01 (0.30), residues: 284
  loop : -0.70 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 629 
 HIS   0.004   0.001   HIS A 563 
 PHE   0.011   0.001   PHE B 317 
 TYR   0.026   0.001   TYR A 605 
 ARG   0.006   0.000   ARG B 172 

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

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

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 156
  time to evaluate  : 1.015 
Fit side-chains
REVERT: B  100 GLN cc_start: 0.8440 (tt0) cc_final: 0.7965 (tm-30)
REVERT: B  101 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7450 (mppt)
REVERT: B  118 ARG cc_start: 0.7353 (ttm-80) cc_final: 0.6542 (mtp180)
REVERT: B  158 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8190 (mt0)
REVERT: B  207 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7214 (mp0)
REVERT: B  297 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8428 (mm)
REVERT: B  570 ASN cc_start: 0.7206 (m-40) cc_final: 0.6868 (m110)
REVERT: B  576 SER cc_start: 0.8455 (m) cc_final: 0.8030 (p)
REVERT: B  577 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.7774 (m-80)
REVERT: B  684 MET cc_start: 0.5796 (tmt) cc_final: 0.5323 (mpm)
REVERT: B  702 LEU cc_start: 0.7639 (tp) cc_final: 0.7281 (tt)
REVERT: B  707 ARG cc_start: 0.7343 (tpp80) cc_final: 0.6847 (mmm160)
REVERT: B  713 MET cc_start: 0.8158 (mmm) cc_final: 0.7898 (mtp)
REVERT: B  738 LYS cc_start: 0.7551 (mttt) cc_final: 0.6752 (mtmm)
REVERT: B  753 MET cc_start: 0.8690 (mmt) cc_final: 0.8086 (mmt)
REVERT: B  815 ASP cc_start: 0.7243 (OUTLIER) cc_final: 0.6690 (p0)
REVERT: A   83 ASN cc_start: 0.8341 (p0) cc_final: 0.8035 (p0)
REVERT: A  118 ARG cc_start: 0.7260 (ttm-80) cc_final: 0.6417 (mtp180)
REVERT: A  207 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7219 (mp0)
REVERT: A  297 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8402 (mm)
REVERT: A  536 TYR cc_start: 0.7630 (m-80) cc_final: 0.7377 (m-80)
REVERT: A  576 SER cc_start: 0.8587 (m) cc_final: 0.8157 (p)
REVERT: A  684 MET cc_start: 0.5650 (tmt) cc_final: 0.5147 (mpm)
REVERT: A  692 LEU cc_start: 0.7204 (mp) cc_final: 0.6988 (mm)
REVERT: A  707 ARG cc_start: 0.7389 (tpp80) cc_final: 0.6884 (mmm160)
REVERT: A  713 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.8099 (mmm)
REVERT: A  753 MET cc_start: 0.8678 (mmt) cc_final: 0.8033 (mmt)
REVERT: A  774 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7842 (mt-10)
  outliers start: 45
  outliers final: 24
  residues processed: 184
  average time/residue: 0.9778
  time to fit residues: 198.5204
Evaluate side-chains
  185 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 152
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  101 LYS
Chi-restraints excluded: chain B residue  158 GLN
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  207 GLU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  239 SER
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  463 VAL
Chi-restraints excluded: chain B residue  577 PHE
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  775 SER
Chi-restraints excluded: chain B residue  782 CYS
Chi-restraints excluded: chain B residue  815 ASP
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  196 ASP
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain A residue  719 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 101 optimal weight:    8.9990
   chunk 92 optimal weight:    9.9990
   chunk 116 optimal weight:    0.9980
   chunk 122 optimal weight:    1.9990
   chunk 4 optimal weight:    0.3980
   chunk 17 optimal weight:    0.2980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B 646 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.152036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.120660 restraints weight = 23004.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 3.69
r_work: 0.3055 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3007
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3007
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10898  Z= 0.251
  Angle     :  0.526   7.423  14868  Z= 0.270
  Chirality :  0.042   0.141   1710
  Planarity :  0.003   0.037   1806
  Dihedral  :  6.999  59.205   1952
  Min Nonbonded Distance : 1.826

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 19.96 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.23), residues: 1268
  helix:  2.60 (0.20), residues: 584
  sheet:  1.15 (0.30), residues: 272
  loop : -0.76 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 629 
 HIS   0.005   0.001   HIS A 563 
 PHE   0.011   0.001   PHE B 632 
 TYR   0.034   0.002   TYR A 605 
 ARG   0.005   0.000   ARG B 172 

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

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

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 154
  time to evaluate  : 1.202 
Fit side-chains
REVERT: B  100 GLN cc_start: 0.8488 (tt0) cc_final: 0.8068 (tm-30)
REVERT: B  101 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7587 (mppt)
REVERT: B  118 ARG cc_start: 0.7277 (ttm-80) cc_final: 0.6545 (mtp180)
REVERT: B  152 MET cc_start: 0.8495 (mtt) cc_final: 0.8149 (mtt)
REVERT: B  158 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8177 (mt0)
REVERT: B  207 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7205 (mp0)
REVERT: B  297 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8395 (mm)
REVERT: B  519 ASP cc_start: 0.6941 (t0) cc_final: 0.6656 (t70)
REVERT: B  570 ASN cc_start: 0.7263 (m-40) cc_final: 0.6908 (m110)
REVERT: B  576 SER cc_start: 0.8461 (m) cc_final: 0.8025 (p)
REVERT: B  684 MET cc_start: 0.5798 (tmt) cc_final: 0.5322 (mpm)
REVERT: B  702 LEU cc_start: 0.7655 (tp) cc_final: 0.7289 (tt)
REVERT: B  707 ARG cc_start: 0.7319 (tpp80) cc_final: 0.6834 (mmm160)
REVERT: B  738 LYS cc_start: 0.7558 (mttt) cc_final: 0.6970 (mtmm)
REVERT: B  753 MET cc_start: 0.8693 (mmt) cc_final: 0.8070 (mmt)
REVERT: A   83 ASN cc_start: 0.8346 (p0) cc_final: 0.8045 (p0)
REVERT: A  118 ARG cc_start: 0.7281 (ttm-80) cc_final: 0.6434 (mtp180)
REVERT: A  158 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8147 (mt0)
REVERT: A  207 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7219 (mp0)
REVERT: A  297 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8484 (mm)
REVERT: A  536 TYR cc_start: 0.7664 (m-80) cc_final: 0.7394 (m-80)
REVERT: A  576 SER cc_start: 0.8602 (m) cc_final: 0.8156 (p)
REVERT: A  684 MET cc_start: 0.5578 (tmt) cc_final: 0.5117 (mpm)
REVERT: A  692 LEU cc_start: 0.7132 (mp) cc_final: 0.6920 (mm)
REVERT: A  707 ARG cc_start: 0.7349 (tpp80) cc_final: 0.6840 (mmm160)
REVERT: A  713 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8120 (mmm)
REVERT: A  753 MET cc_start: 0.8674 (mmt) cc_final: 0.8033 (mmt)
REVERT: A  774 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7819 (mt-10)
  outliers start: 43
  outliers final: 29
  residues processed: 179
  average time/residue: 0.9513
  time to fit residues: 187.7625
Evaluate side-chains
  190 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 153
  time to evaluate  : 1.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  101 LYS
Chi-restraints excluded: chain B residue  158 GLN
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  207 GLU
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  239 SER
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  463 VAL
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  596 ASP
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  775 SER
Chi-restraints excluded: chain B residue  782 CYS
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  158 GLN
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  196 ASP
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  596 ASP
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain A residue  719 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 100 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 4 optimal weight:    0.4980
   chunk 31 optimal weight:    7.9990
   chunk 119 optimal weight:    0.0970
   chunk 116 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
B 646 GLN
A 178 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.153274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.119965 restraints weight = 15337.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 2.05
r_work: 0.3144 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2998
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2998 r_free = 0.2998    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2998 r_free = 0.2998    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2998
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10898  Z= 0.203
  Angle     :  0.494   7.026  14868  Z= 0.255
  Chirality :  0.041   0.140   1710
  Planarity :  0.003   0.038   1806
  Dihedral  :  6.868  58.751   1952
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 20.23 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.23), residues: 1268
  helix:  2.70 (0.20), residues: 584
  sheet:  1.25 (0.30), residues: 268
  loop : -0.73 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 629 
 HIS   0.004   0.001   HIS A 563 
 PHE   0.011   0.001   PHE B 317 
 TYR   0.041   0.002   TYR B 605 
 ARG   0.005   0.000   ARG B 172 

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

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

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 152
  time to evaluate  : 1.156 
Fit side-chains
REVERT: B  101 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7514 (mppt)
REVERT: B  118 ARG cc_start: 0.7319 (ttm-80) cc_final: 0.6460 (mtp180)
REVERT: B  152 MET cc_start: 0.8503 (mtt) cc_final: 0.8190 (mtt)
REVERT: B  158 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8207 (mt0)
REVERT: B  207 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7158 (mp0)
REVERT: B  297 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8409 (mm)
REVERT: B  554 MET cc_start: 0.8237 (mmp) cc_final: 0.8028 (mmm)
REVERT: B  570 ASN cc_start: 0.7233 (m-40) cc_final: 0.6886 (m110)
REVERT: B  576 SER cc_start: 0.8423 (m) cc_final: 0.7964 (p)
REVERT: B  577 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.7776 (m-80)
REVERT: B  684 MET cc_start: 0.5801 (tmt) cc_final: 0.5270 (mpm)
REVERT: B  702 LEU cc_start: 0.7623 (tp) cc_final: 0.7270 (tt)
REVERT: B  707 ARG cc_start: 0.7327 (tpp80) cc_final: 0.6807 (mmm160)
REVERT: B  713 MET cc_start: 0.8089 (mmm) cc_final: 0.7849 (mtp)
REVERT: B  720 ASN cc_start: 0.7983 (m110) cc_final: 0.7687 (m110)
REVERT: B  738 LYS cc_start: 0.7425 (mttt) cc_final: 0.6951 (mtmm)
REVERT: B  753 MET cc_start: 0.8666 (mmt) cc_final: 0.8086 (mmt)
REVERT: A   83 ASN cc_start: 0.8238 (p0) cc_final: 0.7949 (p0)
REVERT: A  118 ARG cc_start: 0.7227 (ttm-80) cc_final: 0.6289 (mtp180)
REVERT: A  158 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8126 (mt0)
REVERT: A  207 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7182 (mp0)
REVERT: A  297 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8394 (mm)
REVERT: A  536 TYR cc_start: 0.7656 (m-80) cc_final: 0.7384 (m-80)
REVERT: A  576 SER cc_start: 0.8564 (m) cc_final: 0.8109 (p)
REVERT: A  684 MET cc_start: 0.5878 (tmt) cc_final: 0.5361 (mpm)
REVERT: A  692 LEU cc_start: 0.7105 (mp) cc_final: 0.6890 (mm)
REVERT: A  707 ARG cc_start: 0.7333 (tpp80) cc_final: 0.6810 (mmm160)
REVERT: A  713 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.8074 (mmm)
REVERT: A  738 LYS cc_start: 0.7171 (mtpm) cc_final: 0.5972 (mmtp)
REVERT: A  753 MET cc_start: 0.8660 (mmt) cc_final: 0.8071 (mmt)
REVERT: A  774 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7787 (mt-10)
  outliers start: 40
  outliers final: 28
  residues processed: 177
  average time/residue: 1.0002
  time to fit residues: 195.0936
Evaluate side-chains
  188 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 151
  time to evaluate  : 1.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  101 LYS
Chi-restraints excluded: chain B residue  158 GLN
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  207 GLU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  239 SER
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  463 VAL
Chi-restraints excluded: chain B residue  577 PHE
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  596 ASP
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  775 SER
Chi-restraints excluded: chain B residue  782 CYS
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  158 GLN
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  196 ASP
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  596 ASP
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain A residue  719 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 110 optimal weight:    4.9990
   chunk 96 optimal weight:    1.9990
   chunk 118 optimal weight:    3.9990
   chunk 99 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9980
   chunk 78 optimal weight:    0.0070
   chunk 90 optimal weight:    0.7980
   overall best weight:    0.9400

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

Flipped N/Q/H residues before XYZ refinement:
B 646 GLN
A 764 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.152177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.119633 restraints weight = 22145.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 3.29
r_work: 0.3042 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3030
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3030
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10898  Z= 0.252
  Angle     :  0.522   6.897  14868  Z= 0.269
  Chirality :  0.042   0.141   1710
  Planarity :  0.003   0.037   1806
  Dihedral  :  6.933  58.642   1952
  Min Nonbonded Distance : 1.829

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 20.05 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.23), residues: 1268
  helix:  2.64 (0.20), residues: 584
  sheet:  1.16 (0.30), residues: 272
  loop : -0.73 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 629 
 HIS   0.004   0.001   HIS A 487 
 PHE   0.012   0.001   PHE B 632 
 TYR   0.037   0.002   TYR B 605 
 ARG   0.005   0.000   ARG B 172 

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

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

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 148
  time to evaluate  : 1.226 
Fit side-chains
REVERT: B  101 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7521 (mppt)
REVERT: B  118 ARG cc_start: 0.7315 (ttm-80) cc_final: 0.6426 (mtp180)
REVERT: B  152 MET cc_start: 0.8470 (mtt) cc_final: 0.8151 (mtt)
REVERT: B  158 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8155 (mt0)
REVERT: B  207 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7151 (mp0)
REVERT: B  297 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8378 (mm)
REVERT: B  519 ASP cc_start: 0.6821 (t0) cc_final: 0.6580 (t70)
REVERT: B  554 MET cc_start: 0.8207 (mmp) cc_final: 0.7978 (mmm)
REVERT: B  570 ASN cc_start: 0.7232 (m-40) cc_final: 0.6883 (m110)
REVERT: B  576 SER cc_start: 0.8426 (m) cc_final: 0.7965 (p)
REVERT: B  577 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.7825 (m-80)
REVERT: B  684 MET cc_start: 0.5763 (tmt) cc_final: 0.5288 (mpm)
REVERT: B  702 LEU cc_start: 0.7525 (tp) cc_final: 0.7198 (tt)
REVERT: B  707 ARG cc_start: 0.7291 (tpp80) cc_final: 0.6785 (mmm160)
REVERT: B  720 ASN cc_start: 0.7981 (m110) cc_final: 0.7683 (m110)
REVERT: B  738 LYS cc_start: 0.7432 (mttt) cc_final: 0.6953 (mtmm)
REVERT: B  753 MET cc_start: 0.8605 (mmt) cc_final: 0.7985 (mmt)
REVERT: A   83 ASN cc_start: 0.8289 (p0) cc_final: 0.7985 (p0)
REVERT: A  118 ARG cc_start: 0.7265 (ttm-80) cc_final: 0.6370 (mtp180)
REVERT: A  158 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8137 (mt0)
REVERT: A  207 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7174 (mp0)
REVERT: A  297 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8444 (mm)
REVERT: A  536 TYR cc_start: 0.7626 (m-80) cc_final: 0.7349 (m-80)
REVERT: A  576 SER cc_start: 0.8557 (m) cc_final: 0.8089 (p)
REVERT: A  684 MET cc_start: 0.5821 (tmt) cc_final: 0.5368 (mpm)
REVERT: A  692 LEU cc_start: 0.7053 (mp) cc_final: 0.6843 (mm)
REVERT: A  707 ARG cc_start: 0.7296 (tpp80) cc_final: 0.6787 (mmm160)
REVERT: A  713 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.8018 (mmm)
REVERT: A  753 MET cc_start: 0.8579 (mmt) cc_final: 0.7962 (mmt)
REVERT: A  774 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7778 (mt-10)
  outliers start: 41
  outliers final: 31
  residues processed: 173
  average time/residue: 0.9817
  time to fit residues: 187.7815
Evaluate side-chains
  187 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 147
  time to evaluate  : 1.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  101 LYS
Chi-restraints excluded: chain B residue  158 GLN
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  207 GLU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  239 SER
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  463 VAL
Chi-restraints excluded: chain B residue  577 PHE
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  596 ASP
Chi-restraints excluded: chain B residue  638 LEU
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  775 SER
Chi-restraints excluded: chain B residue  782 CYS
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  158 GLN
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  196 ASP
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  596 ASP
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain A residue  719 CYS
Chi-restraints excluded: chain A residue  764 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 48 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 31 optimal weight:    7.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
B 646 GLN
A 764 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.152147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.118726 restraints weight = 18835.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 2.81
r_work: 0.3075 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2936 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2925
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2925 r_free = 0.2925    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2925 r_free = 0.2925    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2925
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10898  Z= 0.258
  Angle     :  0.527   6.852  14868  Z= 0.271
  Chirality :  0.042   0.141   1710
  Planarity :  0.003   0.038   1806
  Dihedral  :  6.941  58.463   1952
  Min Nonbonded Distance : 1.830

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 19.88 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.23), residues: 1268
  helix:  2.62 (0.20), residues: 584
  sheet:  1.24 (0.30), residues: 268
  loop : -0.77 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 629 
 HIS   0.004   0.001   HIS A 487 
 PHE   0.015   0.002   PHE A 697 
 TYR   0.036   0.002   TYR B 605 
 ARG   0.005   0.000   ARG B 172 

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

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

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2536 Ramachandran restraints generated.
    1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 149
  time to evaluate  : 1.162 
Fit side-chains
REVERT: B  101 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7607 (mppt)
REVERT: B  118 ARG cc_start: 0.7385 (ttm-80) cc_final: 0.6423 (mtp180)
REVERT: B  152 MET cc_start: 0.8567 (mtt) cc_final: 0.8258 (mtt)
REVERT: B  158 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8273 (mt0)
REVERT: B  207 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7195 (mp0)
REVERT: B  297 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8410 (mm)
REVERT: B  519 ASP cc_start: 0.7043 (t0) cc_final: 0.6761 (t70)
REVERT: B  554 MET cc_start: 0.8348 (mmp) cc_final: 0.8134 (mmm)
REVERT: B  570 ASN cc_start: 0.7350 (m-40) cc_final: 0.6993 (m110)
REVERT: B  576 SER cc_start: 0.8487 (m) cc_final: 0.8028 (p)
REVERT: B  577 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.7886 (m-80)
REVERT: B  684 MET cc_start: 0.5875 (tmt) cc_final: 0.5304 (mpm)
REVERT: B  702 LEU cc_start: 0.7574 (tp) cc_final: 0.7245 (tt)
REVERT: B  707 ARG cc_start: 0.7382 (tpp80) cc_final: 0.6824 (mmm160)
REVERT: B  720 ASN cc_start: 0.8091 (m110) cc_final: 0.7802 (m110)
REVERT: B  738 LYS cc_start: 0.7510 (mttt) cc_final: 0.7038 (mtmm)
REVERT: B  753 MET cc_start: 0.8689 (mmt) cc_final: 0.8113 (mmt)
REVERT: A   83 ASN cc_start: 0.8454 (p0) cc_final: 0.8176 (p0)
REVERT: A  118 ARG cc_start: 0.7349 (ttm-80) cc_final: 0.6387 (mtp180)
REVERT: A  158 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8249 (mt0)
REVERT: A  207 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7234 (mp0)
REVERT: A  297 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8497 (mm)
REVERT: A  536 TYR cc_start: 0.7695 (m-80) cc_final: 0.7431 (m-80)
REVERT: A  576 SER cc_start: 0.8627 (m) cc_final: 0.8158 (p)
REVERT: A  684 MET cc_start: 0.5934 (tmt) cc_final: 0.5379 (mpm)
REVERT: A  692 LEU cc_start: 0.7148 (mp) cc_final: 0.6935 (mm)
REVERT: A  707 ARG cc_start: 0.7402 (tpp80) cc_final: 0.6837 (mmm160)
REVERT: A  713 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8121 (mmm)
REVERT: A  753 MET cc_start: 0.8661 (mmt) cc_final: 0.8084 (mmt)
REVERT: A  774 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7926 (mt-10)
  outliers start: 43
  outliers final: 31
  residues processed: 175
  average time/residue: 0.9590
  time to fit residues: 184.9269
Evaluate side-chains
  188 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 148
  time to evaluate  : 1.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  101 LYS
Chi-restraints excluded: chain B residue  158 GLN
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain B residue  204 VAL
Chi-restraints excluded: chain B residue  207 GLU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  239 SER
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  463 VAL
Chi-restraints excluded: chain B residue  577 PHE
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  596 ASP
Chi-restraints excluded: chain B residue  638 LEU
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  775 SER
Chi-restraints excluded: chain B residue  782 CYS
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  158 GLN
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  196 ASP
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  596 ASP
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain A residue  719 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 127 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 71 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 124 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
B 646 GLN
A 764 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.152546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.120836 restraints weight = 27725.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 4.26
r_work: 0.3020 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2984
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2984 r_free = 0.2984    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2984 r_free = 0.2984    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2984
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10898  Z= 0.230
  Angle     :  0.513   7.995  14868  Z= 0.264
  Chirality :  0.042   0.141   1710
  Planarity :  0.003   0.038   1806
  Dihedral  :  6.910  58.001   1952
  Min Nonbonded Distance : 1.836

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 20.05 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.95 (0.23), residues: 1268
  helix:  2.66 (0.20), residues: 584
  sheet:  1.26 (0.31), residues: 268
  loop : -0.74 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 629 
 HIS   0.004   0.001   HIS A 563 
 PHE   0.011   0.001   PHE B 632 
 TYR   0.033   0.002   TYR B 605 
 ARG   0.005   0.000   ARG B 172 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7924.96 seconds
wall clock time: 140 minutes 38.02 seconds (8438.02 seconds total)