Starting phenix.real_space_refine
on Sat Aug 23 07:38:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j6m_36008/08_2025/8j6m_36008.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j6m_36008/08_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_36008/08_2025/8j6m_36008.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j6m_36008/08_2025/8j6m_36008.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j6m_36008/08_2025/8j6m_36008.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j6m_36008/08_2025/8j6m_36008.cif"
  }
  resolution = 2.77
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.153
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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, 'ASP:plan': 1, 'TRP: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, 'ASP:plan': 1, 'TRP: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, 'ASP:plan': 1, 'TRP: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, 'ASP:plan': 1, 'TRP: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: 5.17, per 1000 atoms: 0.49
  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: 0.96
  Conformation dependent library (CDL) restraints added in 889.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  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: 0.35
  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: 1.97

  Time building geometry restraints manager: 1.29 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:             3.440
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     16.310
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.050
  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:             0.020
  Load rotamer database and sin/cos tables:9.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.050
-------------------------------------------------------------------------------
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      :  0.009   0.226  10912  Z= 0.561
  Angle     :  1.110  11.972  14884  Z= 0.701
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.007   0.001   ARG A 289 
 TYR   0.021   0.002   TYR B 605 
 PHE   0.023   0.002   PHE A 317 
 TRP   0.016   0.002   TRP A 106 
 HIS   0.004   0.001   HIS A 636 

Details of bonding type rmsd
  covalent geometry    : bond        0.00789 (10898)
  covalent geometry    : angle       1.10424 (14868)
  SS BOND              : bond        0.01515 (    8)
  SS BOND              : angle       3.71678 (   16)
  hydrogen bonds       : bond        0.19433 (  634)
  hydrogen bonds       : angle       7.38516 ( 1822)
  metal coordination   : bond        0.16225 (    6)

*********************** 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  : 0.400 
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: 0.5296 (mpp)
REVERT: B  702 LEU cc_start: 0.7717 (tp) cc_final: 0.7303 (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: 0.5114 (mpp)
REVERT: A  707 ARG cc_start: 0.7280 (tpp80) cc_final: 0.6967 (mmm160)
REVERT: A  774 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7658 (mt-10)
  outliers start: 18
  outliers final: 9
  residues processed: 203
  average time/residue: 0.5066
  time to fit residues: 111.5860
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  : 0.304 
-------------------------------------------------------------------------------
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 98 optimal weight:    0.9980
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    0.2980
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 636 HIS
A 646 GLN
A 694 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.153942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.120718 restraints weight = 13538.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 1.90
r_work: 0.3178 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3026
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3026 r_free = 0.3026    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3026 r_free = 0.3026    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3026
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.1481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  10912  Z= 0.167
  Angle     :  0.610   7.556  14884  Z= 0.310
  Chirality :  0.045   0.153   1710
  Planarity :  0.004   0.035   1806
  Dihedral  :  8.585  56.557   1964
  Min Nonbonded Distance : 1.790

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 18.20 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.64 (0.22), residues: 1268
  helix:  2.21 (0.19), residues: 584
  sheet:  1.32 (0.28), residues: 284
  loop : -0.82 (0.28), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 172 
 TYR   0.016   0.002   TYR B 605 
 PHE   0.022   0.002   PHE A 317 
 TRP   0.013   0.001   TRP A 629 
 HIS   0.005   0.001   HIS B 795 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (10898)
  covalent geometry    : angle       0.60674 (14868)
  SS BOND              : bond        0.00286 (    8)
  SS BOND              : angle       2.13377 (   16)
  hydrogen bonds       : bond        0.05195 (  634)
  hydrogen bonds       : angle       4.96679 ( 1822)
  metal coordination   : bond        0.01733 (    6)

*********************** 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
  204 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 170
  time to evaluate  : 0.442 
Fit side-chains
REVERT: B   61 GLU cc_start: 0.8340 (tt0) cc_final: 0.8107 (tt0)
REVERT: B   90 ASN cc_start: 0.7865 (m-40) cc_final: 0.7651 (m-40)
REVERT: B  118 ARG cc_start: 0.7307 (ttm-80) cc_final: 0.6641 (mtp180)
REVERT: B  158 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7906 (mt0)
REVERT: B  274 SER cc_start: 0.7423 (m) cc_final: 0.7180 (t)
REVERT: B  536 TYR cc_start: 0.7362 (m-80) cc_final: 0.7147 (m-80)
REVERT: B  576 SER cc_start: 0.8331 (m) cc_final: 0.8001 (p)
REVERT: B  684 MET cc_start: 0.5758 (tmt) cc_final: 0.4975 (mpm)
REVERT: B  702 LEU cc_start: 0.7580 (tp) cc_final: 0.7212 (tt)
REVERT: B  707 ARG cc_start: 0.7214 (tpp80) cc_final: 0.6786 (mmm160)
REVERT: B  738 LYS cc_start: 0.7637 (mttt) cc_final: 0.7191 (mtpm)
REVERT: A  118 ARG cc_start: 0.7394 (ttm-80) cc_final: 0.6498 (mtp180)
REVERT: A  158 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7863 (mt0)
REVERT: A  302 LYS cc_start: 0.7889 (mptm) cc_final: 0.7592 (mmtm)
REVERT: A  536 TYR cc_start: 0.7410 (m-80) cc_final: 0.7118 (m-80)
REVERT: A  576 SER cc_start: 0.8301 (m) cc_final: 0.7986 (p)
REVERT: A  684 MET cc_start: 0.5525 (tmt) cc_final: 0.4836 (mpp)
REVERT: A  692 LEU cc_start: 0.7237 (mp) cc_final: 0.7023 (mp)
REVERT: A  697 PHE cc_start: 0.7584 (t80) cc_final: 0.7379 (t80)
REVERT: A  707 ARG cc_start: 0.7221 (tpp80) cc_final: 0.6743 (mmm160)
REVERT: A  738 LYS cc_start: 0.6937 (mtpm) cc_final: 0.5726 (mmtp)
REVERT: A  774 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7815 (mt-10)
  outliers start: 34
  outliers final: 19
  residues processed: 190
  average time/residue: 0.4412
  time to fit residues: 92.0190
Evaluate side-chains
  177 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 156
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
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  296 THR
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 106 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 70 optimal weight:    0.5980
   chunk 92 optimal weight:    9.9990
   chunk 56 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.7580

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.153572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.119971 restraints weight = 15037.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 2.01
r_work: 0.3162 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3013
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3013 r_free = 0.3013    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 = 0.3013 r_free = 0.3013    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3013
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10912  Z= 0.148
  Angle     :  0.533   6.601  14884  Z= 0.275
  Chirality :  0.043   0.143   1710
  Planarity :  0.003   0.036   1806
  Dihedral  :  7.256  56.049   1956
  Min Nonbonded Distance : 1.832

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 19.17 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.86 (0.22), residues: 1268
  helix:  2.53 (0.20), residues: 584
  sheet:  1.18 (0.28), residues: 284
  loop : -0.74 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 172 
 TYR   0.019   0.002   TYR A 605 
 PHE   0.015   0.001   PHE A 317 
 TRP   0.011   0.001   TRP A 106 
 HIS   0.005   0.001   HIS B 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (10898)
  covalent geometry    : angle       0.52992 (14868)
  SS BOND              : bond        0.00169 (    8)
  SS BOND              : angle       1.78464 (   16)
  hydrogen bonds       : bond        0.04569 (  634)
  hydrogen bonds       : angle       4.61871 ( 1822)
  metal coordination   : bond        0.00760 (    6)

*********************** 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: 34
    poor density    : 169
  time to evaluate  : 0.309 
Fit side-chains
REVERT: B  118 ARG cc_start: 0.7308 (ttm-80) cc_final: 0.6525 (mtp180)
REVERT: B  297 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8494 (mm)
REVERT: B  576 SER cc_start: 0.8520 (m) cc_final: 0.8118 (p)
REVERT: B  684 MET cc_start: 0.5576 (tmt) cc_final: 0.5189 (mpp)
REVERT: B  702 LEU cc_start: 0.7594 (tp) cc_final: 0.7228 (tt)
REVERT: B  707 ARG cc_start: 0.7245 (tpp80) cc_final: 0.6855 (mmm160)
REVERT: B  738 LYS cc_start: 0.7742 (mttt) cc_final: 0.7228 (mtmm)
REVERT: A  118 ARG cc_start: 0.7256 (ttm-80) cc_final: 0.6383 (mtp180)
REVERT: A  302 LYS cc_start: 0.7855 (mptm) cc_final: 0.7560 (mmmm)
REVERT: A  536 TYR cc_start: 0.7443 (m-80) cc_final: 0.7131 (m-80)
REVERT: A  576 SER cc_start: 0.8418 (m) cc_final: 0.8030 (p)
REVERT: A  684 MET cc_start: 0.5415 (tmt) cc_final: 0.5011 (mpm)
REVERT: A  692 LEU cc_start: 0.7366 (mp) cc_final: 0.7116 (mp)
REVERT: A  697 PHE cc_start: 0.7553 (t80) cc_final: 0.7341 (t80)
REVERT: A  707 ARG cc_start: 0.7246 (tpp80) cc_final: 0.6839 (mmm160)
REVERT: A  738 LYS cc_start: 0.6969 (mtpm) cc_final: 0.6145 (mtmm)
REVERT: A  774 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7881 (mt-10)
  outliers start: 34
  outliers final: 18
  residues processed: 186
  average time/residue: 0.4194
  time to fit residues: 86.0570
Evaluate side-chains
  178 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 159
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
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  296 THR
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  596 ASP
Chi-restraints excluded: chain B residue  641 LEU
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  463 VAL
Chi-restraints excluded: chain A residue  587 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9980
   chunk 37 optimal weight:    7.9990
   chunk 127 optimal weight:    0.4980
   chunk 40 optimal weight:    2.9990
   chunk 95 optimal weight:    0.2980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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
B 720 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.154068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.120585 restraints weight = 14397.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 1.96
r_work: 0.3170 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3012
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3012
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10912  Z= 0.135
  Angle     :  0.504   7.163  14884  Z= 0.260
  Chirality :  0.042   0.140   1710
  Planarity :  0.003   0.035   1806
  Dihedral  :  7.060  58.562   1953
  Min Nonbonded Distance : 1.840

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 18.99 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.97 (0.23), residues: 1268
  helix:  2.66 (0.20), residues: 584
  sheet:  1.18 (0.29), residues: 284
  loop : -0.71 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 172 
 TYR   0.023   0.001   TYR A 605 
 PHE   0.013   0.001   PHE A 317 
 TRP   0.010   0.001   TRP A 106 
 HIS   0.004   0.001   HIS A 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (10898)
  covalent geometry    : angle       0.50095 (14868)
  SS BOND              : bond        0.00215 (    8)
  SS BOND              : angle       1.67596 (   16)
  hydrogen bonds       : bond        0.04156 (  634)
  hydrogen bonds       : angle       4.50314 ( 1822)
  metal coordination   : bond        0.00645 (    6)

*********************** 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
  200 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 161
  time to evaluate  : 0.333 
Fit side-chains
REVERT: B  118 ARG cc_start: 0.7289 (ttm-80) cc_final: 0.6480 (mtp180)
REVERT: B  158 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8245 (mt0)
REVERT: B  297 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8462 (mm)
REVERT: B  576 SER cc_start: 0.8443 (m) cc_final: 0.8045 (p)
REVERT: B  684 MET cc_start: 0.5550 (tmt) cc_final: 0.5091 (mpm)
REVERT: B  702 LEU cc_start: 0.7621 (tp) cc_final: 0.7261 (tt)
REVERT: B  707 ARG cc_start: 0.7215 (tpp80) cc_final: 0.6773 (mmm160)
REVERT: B  738 LYS cc_start: 0.7534 (mttt) cc_final: 0.6742 (mtmm)
REVERT: B  815 ASP cc_start: 0.7194 (OUTLIER) cc_final: 0.6646 (p0)
REVERT: A  118 ARG cc_start: 0.7189 (ttm-80) cc_final: 0.6321 (mtp180)
REVERT: A  158 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8227 (mt0)
REVERT: A  536 TYR cc_start: 0.7477 (m-80) cc_final: 0.7205 (m-80)
REVERT: A  576 SER cc_start: 0.8573 (m) cc_final: 0.8164 (p)
REVERT: A  684 MET cc_start: 0.5363 (tmt) cc_final: 0.4931 (mpm)
REVERT: A  692 LEU cc_start: 0.7229 (mp) cc_final: 0.6975 (mm)
REVERT: A  707 ARG cc_start: 0.7296 (tpp80) cc_final: 0.6876 (mmm160)
REVERT: A  713 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8066 (mmm)
REVERT: A  738 LYS cc_start: 0.7004 (mtpm) cc_final: 0.6163 (mtmm)
REVERT: A  753 MET cc_start: 0.8578 (mmt) cc_final: 0.7796 (mmt)
REVERT: A  774 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7808 (mt-10)
  outliers start: 39
  outliers final: 26
  residues processed: 182
  average time/residue: 0.4251
  time to fit residues: 85.0886
Evaluate side-chains
  184 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 153
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
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  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  587 LEU
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  713 MET
Chi-restraints excluded: chain B residue  815 ASP
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  221 MET
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  459 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  713 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 9 optimal weight:    7.9990
   chunk 39 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 95 optimal weight:    6.9990
   chunk 4 optimal weight:    2.9990
   chunk 113 optimal weight:    6.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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 = 0.3635 r_free = 0.3635 target = 0.146929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.113193 restraints weight = 17325.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 2.37
r_work: 0.3046 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2880
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2880
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.099  10912  Z= 0.393
  Angle     :  0.755  10.305  14884  Z= 0.381
  Chirality :  0.052   0.191   1710
  Planarity :  0.005   0.053   1806
  Dihedral  :  7.723  59.800   1951
  Min Nonbonded Distance : 1.768

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 18.64 %
    Favored  : 76.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.22), residues: 1268
  helix:  1.85 (0.20), residues: 584
  sheet:  1.14 (0.30), residues: 272
  loop : -1.12 (0.27), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  79 
 TYR   0.031   0.003   TYR A 605 
 PHE   0.018   0.003   PHE B 320 
 TRP   0.014   0.003   TRP B 629 
 HIS   0.008   0.002   HIS A 487 

Details of bonding type rmsd
  covalent geometry    : bond        0.00968 (10898)
  covalent geometry    : angle       0.74893 (14868)
  SS BOND              : bond        0.00617 (    8)
  SS BOND              : angle       3.03668 (   16)
  hydrogen bonds       : bond        0.05778 (  634)
  hydrogen bonds       : angle       4.99701 ( 1822)
  metal coordination   : bond        0.01055 (    6)

*********************** 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
  198 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 147
  time to evaluate  : 0.415 
Fit side-chains
REVERT: B  101 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7531 (mppt)
REVERT: B  118 ARG cc_start: 0.7474 (ttm-80) cc_final: 0.6676 (mtp180)
REVERT: B  158 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7923 (mt0)
REVERT: B  207 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7244 (mp0)
REVERT: B  274 SER cc_start: 0.7275 (OUTLIER) cc_final: 0.6964 (t)
REVERT: B  576 SER cc_start: 0.8624 (m) cc_final: 0.8190 (p)
REVERT: B  684 MET cc_start: 0.5732 (tmt) cc_final: 0.5215 (mpm)
REVERT: B  702 LEU cc_start: 0.7687 (tp) cc_final: 0.7361 (tt)
REVERT: B  707 ARG cc_start: 0.7426 (tpp80) cc_final: 0.6785 (mmm160)
REVERT: B  738 LYS cc_start: 0.7815 (mttt) cc_final: 0.7364 (mtpm)
REVERT: A   83 ASN cc_start: 0.8711 (p0) cc_final: 0.8261 (p0)
REVERT: A  118 ARG cc_start: 0.7378 (ttm-80) cc_final: 0.6476 (mtp180)
REVERT: A  158 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7915 (mt0)
REVERT: A  207 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7316 (mp0)
REVERT: A  297 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8313 (mm)
REVERT: A  519 ASP cc_start: 0.7309 (t0) cc_final: 0.6966 (t0)
REVERT: A  524 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6527 (mtt180)
REVERT: A  536 TYR cc_start: 0.7591 (m-80) cc_final: 0.7355 (m-80)
REVERT: A  576 SER cc_start: 0.8531 (m) cc_final: 0.8100 (p)
REVERT: A  684 MET cc_start: 0.5586 (tmt) cc_final: 0.5054 (mpm)
REVERT: A  692 LEU cc_start: 0.7216 (mp) cc_final: 0.6894 (mm)
REVERT: A  702 LEU cc_start: 0.7670 (tp) cc_final: 0.7289 (tt)
REVERT: A  707 ARG cc_start: 0.7428 (tpp80) cc_final: 0.6767 (mmm160)
REVERT: A  713 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8158 (mmm)
REVERT: A  774 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7880 (mt-10)
  outliers start: 51
  outliers final: 30
  residues processed: 174
  average time/residue: 0.3904
  time to fit residues: 74.5625
Evaluate side-chains
  186 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 147
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
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  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  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  638 LEU
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  713 MET
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  155 LEU
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  457 LEU
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 41 optimal weight:    0.9990
   chunk 116 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9990
   chunk 127 optimal weight:    0.4980
   chunk 55 optimal weight:    0.0970
   chunk 7 optimal weight:    0.3980
   chunk 12 optimal weight:    0.6980
   chunk 98 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
B 475 ASN
B 570 ASN
B 646 GLN
B 720 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.152325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.119541 restraints weight = 20526.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 3.09
r_work: 0.3081 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3070
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3069
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10912  Z= 0.127
  Angle     :  0.511   6.938  14884  Z= 0.264
  Chirality :  0.042   0.140   1710
  Planarity :  0.003   0.039   1806
  Dihedral  :  7.174  59.514   1951
  Min Nonbonded Distance : 1.826

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 20.49 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.70 (0.23), residues: 1268
  helix:  2.46 (0.20), residues: 584
  sheet:  1.13 (0.30), residues: 272
  loop : -0.89 (0.28), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 172 
 TYR   0.020   0.001   TYR A 605 
 PHE   0.012   0.001   PHE A 317 
 TRP   0.009   0.001   TRP A 106 
 HIS   0.004   0.001   HIS A 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (10898)
  covalent geometry    : angle       0.50786 (14868)
  SS BOND              : bond        0.00274 (    8)
  SS BOND              : angle       1.76472 (   16)
  hydrogen bonds       : bond        0.04143 (  634)
  hydrogen bonds       : angle       4.55765 ( 1822)
  metal coordination   : bond        0.00673 (    6)

*********************** 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
  191 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 157
  time to evaluate  : 0.430 
Fit side-chains
REVERT: B  118 ARG cc_start: 0.7356 (ttm-80) cc_final: 0.6585 (mtp180)
REVERT: B  158 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8094 (mt0)
REVERT: B  207 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7178 (mp0)
REVERT: B  274 SER cc_start: 0.7259 (OUTLIER) cc_final: 0.7046 (t)
REVERT: B  297 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8358 (mm)
REVERT: B  576 SER cc_start: 0.8468 (m) cc_final: 0.8038 (p)
REVERT: B  684 MET cc_start: 0.5706 (tmt) cc_final: 0.5300 (mpm)
REVERT: B  702 LEU cc_start: 0.7625 (tp) cc_final: 0.7320 (tt)
REVERT: B  707 ARG cc_start: 0.7298 (tpp80) cc_final: 0.6809 (mmm160)
REVERT: B  738 LYS cc_start: 0.7472 (mttt) cc_final: 0.6886 (mtmm)
REVERT: B  753 MET cc_start: 0.8622 (mmt) cc_final: 0.8046 (mmt)
REVERT: A  118 ARG cc_start: 0.7224 (ttm-80) cc_final: 0.6532 (mtp180)
REVERT: A  158 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8101 (mt0)
REVERT: A  207 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7192 (mp0)
REVERT: A  536 TYR cc_start: 0.7600 (m-80) cc_final: 0.7343 (m-80)
REVERT: A  576 SER cc_start: 0.8367 (m) cc_final: 0.7950 (p)
REVERT: A  684 MET cc_start: 0.5587 (tmt) cc_final: 0.5176 (mpm)
REVERT: A  692 LEU cc_start: 0.7041 (mp) cc_final: 0.6828 (mm)
REVERT: A  702 LEU cc_start: 0.7541 (tp) cc_final: 0.7159 (tt)
REVERT: A  707 ARG cc_start: 0.7311 (tpp80) cc_final: 0.6817 (mmm160)
REVERT: A  713 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7971 (mmm)
REVERT: A  753 MET cc_start: 0.8592 (mmt) cc_final: 0.7820 (mmt)
REVERT: A  774 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7696 (mt-10)
  outliers start: 34
  outliers final: 22
  residues processed: 179
  average time/residue: 0.4493
  time to fit residues: 88.6834
Evaluate side-chains
  178 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 149
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
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  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  596 ASP
Chi-restraints excluded: chain B residue  641 LEU
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  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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 115 optimal weight:    2.9990
   chunk 121 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 9 optimal weight:    7.9990
   chunk 114 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 86 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   overall best weight:    1.3586

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.149979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.118035 restraints weight = 22928.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 3.37
r_work: 0.3004 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3002
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3002
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  10912  Z= 0.206
  Angle     :  0.570   7.784  14884  Z= 0.291
  Chirality :  0.044   0.143   1710
  Planarity :  0.004   0.038   1806
  Dihedral  :  7.268  59.952   1951
  Min Nonbonded Distance : 1.806

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 19.43 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.23), residues: 1268
  helix:  2.39 (0.20), residues: 584
  sheet:  1.10 (0.30), residues: 272
  loop : -0.90 (0.28), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 593 
 TYR   0.027   0.002   TYR B 605 
 PHE   0.012   0.002   PHE B 632 
 TRP   0.010   0.002   TRP B 629 
 HIS   0.005   0.001   HIS B 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 (10898)
  covalent geometry    : angle       0.56580 (14868)
  SS BOND              : bond        0.00324 (    8)
  SS BOND              : angle       2.15081 (   16)
  hydrogen bonds       : bond        0.04572 (  634)
  hydrogen bonds       : angle       4.62212 ( 1822)
  metal coordination   : bond        0.00815 (    6)

*********************** 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
  190 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 145
  time to evaluate  : 0.412 
Fit side-chains
REVERT: B  101 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7636 (mppt)
REVERT: B  118 ARG cc_start: 0.7362 (ttm-80) cc_final: 0.6562 (mtp180)
REVERT: B  152 MET cc_start: 0.8453 (mtt) cc_final: 0.8060 (mtt)
REVERT: B  158 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8180 (mt0)
REVERT: B  207 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7248 (mp0)
REVERT: B  274 SER cc_start: 0.7240 (OUTLIER) cc_final: 0.7022 (t)
REVERT: B  297 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8401 (mm)
REVERT: B  576 SER cc_start: 0.8515 (m) cc_final: 0.8067 (p)
REVERT: B  684 MET cc_start: 0.5765 (tmt) cc_final: 0.5307 (mpm)
REVERT: B  702 LEU cc_start: 0.7561 (tp) cc_final: 0.7258 (tt)
REVERT: B  707 ARG cc_start: 0.7335 (tpp80) cc_final: 0.6824 (mmm160)
REVERT: B  738 LYS cc_start: 0.7659 (mttt) cc_final: 0.7152 (mtmm)
REVERT: A  118 ARG cc_start: 0.7295 (ttm-80) cc_final: 0.6481 (mtp180)
REVERT: A  158 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8187 (mt0)
REVERT: A  207 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7222 (mp0)
REVERT: A  297 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8264 (mm)
REVERT: A  536 TYR cc_start: 0.7597 (m-80) cc_final: 0.7333 (m-80)
REVERT: A  576 SER cc_start: 0.8405 (m) cc_final: 0.7957 (p)
REVERT: A  684 MET cc_start: 0.5580 (tmt) cc_final: 0.5123 (mpm)
REVERT: A  692 LEU cc_start: 0.7090 (mp) cc_final: 0.6871 (mm)
REVERT: A  702 LEU cc_start: 0.7571 (tp) cc_final: 0.7211 (tt)
REVERT: A  707 ARG cc_start: 0.7330 (tpp80) cc_final: 0.6795 (mmm160)
REVERT: A  713 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8054 (mmm)
REVERT: A  774 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7763 (mt-10)
  outliers start: 45
  outliers final: 24
  residues processed: 173
  average time/residue: 0.4504
  time to fit residues: 85.3132
Evaluate side-chains
  177 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 144
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
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  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  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  596 ASP
Chi-restraints excluded: chain B residue  641 LEU
Chi-restraints excluded: chain B residue  713 MET
Chi-restraints excluded: chain B residue  782 CYS
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  155 LEU
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  457 LEU
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  764 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9990
   chunk 121 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 68 optimal weight:    0.0010
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.7388

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.151779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.118862 restraints weight = 12415.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.82
r_work: 0.3158 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3019
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3019 r_free = 0.3019    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3019 r_free = 0.3019    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3019
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10912  Z= 0.146
  Angle     :  0.525   7.228  14884  Z= 0.269
  Chirality :  0.042   0.141   1710
  Planarity :  0.003   0.037   1806
  Dihedral  :  7.136  59.595   1951
  Min Nonbonded Distance : 1.823

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 19.70 %
    Favored  : 76.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.78 (0.23), residues: 1268
  helix:  2.54 (0.20), residues: 584
  sheet:  1.08 (0.30), residues: 272
  loop : -0.79 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 172 
 TYR   0.023   0.002   TYR A 605 
 PHE   0.011   0.001   PHE B 632 
 TRP   0.009   0.001   TRP B 629 
 HIS   0.004   0.001   HIS A 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (10898)
  covalent geometry    : angle       0.52145 (14868)
  SS BOND              : bond        0.00297 (    8)
  SS BOND              : angle       1.89255 (   16)
  hydrogen bonds       : bond        0.04185 (  634)
  hydrogen bonds       : angle       4.54018 ( 1822)
  metal coordination   : bond        0.00720 (    6)

*********************** 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
  186 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 148
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
REVERT: B  118 ARG cc_start: 0.7369 (ttm-80) cc_final: 0.6554 (mtp180)
REVERT: B  152 MET cc_start: 0.8490 (mtt) cc_final: 0.8148 (mtt)
REVERT: B  158 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8216 (mt0)
REVERT: B  207 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7232 (mp0)
REVERT: B  297 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8414 (mm)
REVERT: B  576 SER cc_start: 0.8485 (m) cc_final: 0.8072 (p)
REVERT: B  577 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.7761 (m-80)
REVERT: B  684 MET cc_start: 0.5770 (tmt) cc_final: 0.5329 (mpm)
REVERT: B  702 LEU cc_start: 0.7639 (tp) cc_final: 0.7336 (tt)
REVERT: B  707 ARG cc_start: 0.7366 (tpp80) cc_final: 0.6858 (mmm160)
REVERT: B  738 LYS cc_start: 0.7533 (mttt) cc_final: 0.7022 (mtmm)
REVERT: A  118 ARG cc_start: 0.7311 (ttm-80) cc_final: 0.6471 (mtp180)
REVERT: A  158 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8220 (mt0)
REVERT: A  207 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7266 (mp0)
REVERT: A  297 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8322 (mm)
REVERT: A  536 TYR cc_start: 0.7701 (m-80) cc_final: 0.7445 (m-80)
REVERT: A  576 SER cc_start: 0.8419 (m) cc_final: 0.7986 (p)
REVERT: A  684 MET cc_start: 0.5638 (tmt) cc_final: 0.5138 (mpm)
REVERT: A  692 LEU cc_start: 0.7205 (mp) cc_final: 0.6997 (mm)
REVERT: A  702 LEU cc_start: 0.7620 (tp) cc_final: 0.7249 (tt)
REVERT: A  707 ARG cc_start: 0.7381 (tpp80) cc_final: 0.6863 (mmm160)
REVERT: A  713 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8146 (mmm)
REVERT: A  753 MET cc_start: 0.8666 (mmt) cc_final: 0.7964 (mmt)
  outliers start: 38
  outliers final: 26
  residues processed: 173
  average time/residue: 0.4284
  time to fit residues: 81.3981
Evaluate side-chains
  181 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 147
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
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  713 MET
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  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  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  764 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 92 optimal weight:    9.9990
   chunk 122 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.3685 r_free = 0.3685 target = 0.151395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.117972 restraints weight = 18643.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 2.72
r_work: 0.3089 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2933
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2933 r_free = 0.2933    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 = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2932
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10912  Z= 0.165
  Angle     :  0.536   7.328  14884  Z= 0.274
  Chirality :  0.043   0.142   1710
  Planarity :  0.003   0.037   1806
  Dihedral  :  7.144  59.315   1951
  Min Nonbonded Distance : 1.819

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 19.88 %
    Favored  : 76.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.76 (0.23), residues: 1268
  helix:  2.51 (0.20), residues: 584
  sheet:  1.08 (0.30), residues: 272
  loop : -0.80 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 172 
 TYR   0.022   0.002   TYR B 605 
 PHE   0.012   0.002   PHE B 632 
 TRP   0.009   0.001   TRP B 629 
 HIS   0.004   0.001   HIS B 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (10898)
  covalent geometry    : angle       0.53272 (14868)
  SS BOND              : bond        0.00278 (    8)
  SS BOND              : angle       1.92045 (   16)
  hydrogen bonds       : bond        0.04264 (  634)
  hydrogen bonds       : angle       4.54883 ( 1822)
  metal coordination   : bond        0.00742 (    6)

*********************** 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
  182 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 145
  time to evaluate  : 0.396 
Fit side-chains
REVERT: B  101 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7776 (mppt)
REVERT: B  118 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.6590 (mtp180)
REVERT: B  158 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8307 (mt0)
REVERT: B  207 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7262 (mp0)
REVERT: B  297 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8429 (mm)
REVERT: B  576 SER cc_start: 0.8510 (m) cc_final: 0.8081 (p)
REVERT: B  577 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.7830 (m-80)
REVERT: B  684 MET cc_start: 0.5892 (tmt) cc_final: 0.5306 (mpm)
REVERT: B  707 ARG cc_start: 0.7378 (tpp80) cc_final: 0.6825 (mmm160)
REVERT: B  738 LYS cc_start: 0.7551 (mttt) cc_final: 0.7031 (mtmm)
REVERT: A  118 ARG cc_start: 0.7356 (ttm-80) cc_final: 0.6477 (mtp180)
REVERT: A  158 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8307 (mt0)
REVERT: A  207 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7278 (mp0)
REVERT: A  297 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8334 (mm)
REVERT: A  454 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.6705 (t80)
REVERT: A  576 SER cc_start: 0.8433 (m) cc_final: 0.7980 (p)
REVERT: A  684 MET cc_start: 0.5940 (tmt) cc_final: 0.5358 (mpm)
REVERT: A  692 LEU cc_start: 0.7205 (mp) cc_final: 0.6991 (mm)
REVERT: A  702 LEU cc_start: 0.7595 (tp) cc_final: 0.7254 (tt)
REVERT: A  707 ARG cc_start: 0.7411 (tpp80) cc_final: 0.6848 (mmm160)
REVERT: A  713 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8143 (mmm)
REVERT: A  753 MET cc_start: 0.8710 (mmt) cc_final: 0.8057 (mmt)
  outliers start: 37
  outliers final: 26
  residues processed: 170
  average time/residue: 0.4251
  time to fit residues: 79.7844
Evaluate side-chains
  181 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 145
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
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  260 VAL
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  713 MET
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  260 VAL
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  454 PHE
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  713 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   chunk 41 optimal weight:    0.7980
   chunk 28 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 44 optimal weight:    6.9990
   chunk 124 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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
A 764 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.151916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.118941 restraints weight = 16469.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.23
r_work: 0.3127 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2983
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2983 r_free = 0.2983    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 = 0.2983 r_free = 0.2983    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2983
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10912  Z= 0.154
  Angle     :  0.523   6.995  14884  Z= 0.268
  Chirality :  0.042   0.141   1710
  Planarity :  0.003   0.037   1806
  Dihedral  :  7.054  58.172   1951
  Min Nonbonded Distance : 1.825

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 19.96 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.23), residues: 1268
  helix:  2.57 (0.20), residues: 584
  sheet:  1.12 (0.30), residues: 272
  loop : -0.76 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 172 
 TYR   0.025   0.002   TYR B 605 
 PHE   0.012   0.001   PHE B 632 
 TRP   0.008   0.001   TRP B 629 
 HIS   0.004   0.001   HIS A 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (10898)
  covalent geometry    : angle       0.51997 (14868)
  SS BOND              : bond        0.00247 (    8)
  SS BOND              : angle       1.80988 (   16)
  hydrogen bonds       : bond        0.04173 (  634)
  hydrogen bonds       : angle       4.52183 ( 1822)
  metal coordination   : bond        0.00709 (    6)

********************** 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
  188 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 149
  time to evaluate  : 0.288 
Fit side-chains
REVERT: B  118 ARG cc_start: 0.7355 (ttm-80) cc_final: 0.6586 (mtp180)
REVERT: B  158 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8230 (mt0)
REVERT: B  207 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7240 (mp0)
REVERT: B  297 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8442 (mm)
REVERT: B  576 SER cc_start: 0.8488 (m) cc_final: 0.8061 (p)
REVERT: B  577 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.7775 (m-80)
REVERT: B  684 MET cc_start: 0.5846 (tmt) cc_final: 0.5323 (mpm)
REVERT: B  702 LEU cc_start: 0.7758 (tp) cc_final: 0.7410 (tt)
REVERT: B  707 ARG cc_start: 0.7350 (tpp80) cc_final: 0.6811 (mmm160)
REVERT: B  738 LYS cc_start: 0.7520 (mttt) cc_final: 0.7005 (mtmm)
REVERT: A  118 ARG cc_start: 0.7250 (ttm-80) cc_final: 0.6423 (mtp180)
REVERT: A  158 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8238 (mt0)
REVERT: A  207 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7281 (mp0)
REVERT: A  576 SER cc_start: 0.8483 (m) cc_final: 0.8036 (p)
REVERT: A  684 MET cc_start: 0.5874 (tmt) cc_final: 0.5350 (mpm)
REVERT: A  692 LEU cc_start: 0.7305 (mp) cc_final: 0.7093 (mm)
REVERT: A  702 LEU cc_start: 0.7611 (tp) cc_final: 0.7251 (tt)
REVERT: A  707 ARG cc_start: 0.7404 (tpp80) cc_final: 0.6860 (mmm160)
REVERT: A  713 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8155 (mmm)
REVERT: A  753 MET cc_start: 0.8698 (mmt) cc_final: 0.8093 (mmt)
  outliers start: 39
  outliers final: 26
  residues processed: 172
  average time/residue: 0.4246
  time to fit residues: 80.1936
Evaluate side-chains
  183 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 150
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 VAL
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  260 VAL
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  713 MET
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  260 VAL
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  459 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  713 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 122 optimal weight:    0.4980
   chunk 61 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 108 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 94 optimal weight:    0.0570
   chunk 102 optimal weight:    0.9980
   overall best weight:    0.6700

-------------------------------------------------------------------------------
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 = 0.3701 r_free = 0.3701 target = 0.152762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.119202 restraints weight = 17148.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 2.40
r_work: 0.3132 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2978
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2978 r_free = 0.2978    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 = 0.2978 r_free = 0.2978    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2978
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.2425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  10912  Z= 0.135
  Angle     :  0.504   6.966  14884  Z= 0.259
  Chirality :  0.041   0.140   1710
  Planarity :  0.003   0.037   1806
  Dihedral  :  6.946  57.829   1951
  Min Nonbonded Distance : 1.831

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 20.41 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.94 (0.23), residues: 1268
  helix:  2.67 (0.20), residues: 584
  sheet:  1.16 (0.30), residues: 272
  loop : -0.71 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 172 
 TYR   0.022   0.002   TYR B 605 
 PHE   0.011   0.001   PHE A 317 
 TRP   0.008   0.001   TRP B 629 
 HIS   0.004   0.001   HIS A 563 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (10898)
  covalent geometry    : angle       0.50137 (14868)
  SS BOND              : bond        0.00238 (    8)
  SS BOND              : angle       1.63715 (   16)
  hydrogen bonds       : bond        0.04004 (  634)
  hydrogen bonds       : angle       4.46579 ( 1822)
  metal coordination   : bond        0.00659 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3870.34 seconds
wall clock time: 66 minutes 47.02 seconds (4007.02 seconds total)