Starting phenix.real_space_refine
on Wed May 21 00:38:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8avd_15679/05_2025/8avd_15679.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8avd_15679/05_2025/8avd_15679.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.42
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8avd_15679/05_2025/8avd_15679.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8avd_15679/05_2025/8avd_15679.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8avd_15679/05_2025/8avd_15679.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8avd_15679/05_2025/8avd_15679.cif"
  }
  resolution = 4.42
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 9439 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ni      3      6.56       5
     S      60      5.16       5
     C    8127      2.51       5
     N    2154      2.21       5
     O    2433      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 12777
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1077
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1077
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 133}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 399, 3181
          Classifications: {'peptide': 399}
          Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 372}
    Chain: "C"
      Number of atoms: 1077
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1077
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 133}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 3181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 399, 3181
          Classifications: {'peptide': 399}
          Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 372}
    Chain: "E"
      Number of atoms: 1077
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1077
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 133}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 3181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 399, 3181
          Classifications: {'peptide': 399}
          Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 372}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' NI': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' NI': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' NI': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.02, per 1000 atoms: 0.55
  Number of scatterers: 12777
  At special positions: 0
  Unit cell: (132.64, 144.246, 126.008, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ni      3     28.00
     S      60     16.00
     O    2433      8.00
     N    2154      7.00
     C    8127      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 117 " - pdb=" SG  CYS A 167 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 350 " - pdb=" SG  CYS B 410 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 411 " - pdb=" SG  CYS B 416 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 434 " - pdb=" SG  CYS B 445 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 471 " - pdb=" SG  CYS B 526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 486 " - pdb=" SG  CYS B 496 " distance=2.06
    Simple disulfide: pdb=" SG  CYS C 117 " - pdb=" SG  CYS C 167 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 350 " - pdb=" SG  CYS D 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 411 " - pdb=" SG  CYS D 416 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 434 " - pdb=" SG  CYS D 445 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 471 " - pdb=" SG  CYS D 526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 486 " - pdb=" SG  CYS D 496 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E 117 " - pdb=" SG  CYS E 167 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 350 " - pdb=" SG  CYS F 410 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 411 " - pdb=" SG  CYS F 416 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 434 " - pdb=" SG  CYS F 445 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 471 " - pdb=" SG  CYS F 526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 486 " - pdb=" SG  CYS F 496 " distance=2.08

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.91
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3102

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 30 sheets defined
      21.2% alpha, 31.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 44
    Processing helix  chain 'A' and resid 45 through 50
      removed outlier: 4.029A  pdb=" N   SER A  50 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 88
      removed outlier: 3.979A  pdb=" N   SER A  88 " --> pdb=" O   GLN A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 116
    Processing helix  chain 'A' and resid 130 through 138
      removed outlier: 3.691A  pdb=" N   VAL A 134 " --> pdb=" O   SER A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 160
    Processing helix  chain 'B' and resid 375 through 377
      No H-bonds generated for 'chain 'B' and resid 375 through 377'
    Processing helix  chain 'B' and resid 528 through 533
      removed outlier: 3.936A  pdb=" N   VAL B 533 " --> pdb=" O   ASP B 530 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 23 through 45
    Processing helix  chain 'C' and resid 45 through 50
      removed outlier: 4.090A  pdb=" N   SER C  50 " --> pdb=" O   SER C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 71 through 89
      removed outlier: 3.930A  pdb=" N   SER C  88 " --> pdb=" O   GLN C  84 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LEU C  89 " --> pdb=" O   VAL C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 116
    Processing helix  chain 'C' and resid 130 through 138
      removed outlier: 3.518A  pdb=" N   VAL C 134 " --> pdb=" O   SER C 130 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 160
    Processing helix  chain 'D' and resid 375 through 377
      No H-bonds generated for 'chain 'D' and resid 375 through 377'
    Processing helix  chain 'D' and resid 528 through 533
      removed outlier: 3.936A  pdb=" N   VAL D 533 " --> pdb=" O   ASP D 530 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 23 through 45
    Processing helix  chain 'E' and resid 45 through 50
      removed outlier: 3.917A  pdb=" N   SER E  50 " --> pdb=" O   SER E  46 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 71 through 89
      removed outlier: 3.892A  pdb=" N   SER E  88 " --> pdb=" O   GLN E  84 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU E  89 " --> pdb=" O   VAL E  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 91 through 116
    Processing helix  chain 'E' and resid 130 through 138
    Processing helix  chain 'E' and resid 138 through 160
    Processing helix  chain 'F' and resid 375 through 377
      No H-bonds generated for 'chain 'F' and resid 375 through 377'
    Processing helix  chain 'F' and resid 528 through 533
      removed outlier: 3.920A  pdb=" N   VAL F 533 " --> pdb=" O   ASP F 530 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58
    Processing sheet with id=AA2, first strand: chain 'B' and resid 240 through 246
      removed outlier: 6.086A  pdb=" N   GLY B 241 " --> pdb=" O   ASP B 257 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   ASP B 257 " --> pdb=" O   GLY B 241 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 279 through 286
    Processing sheet with id=AA4, first strand: chain 'B' and resid 331 through 334
    Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 341
      removed outlier: 3.546A  pdb=" N   ILE B 338 " --> pdb=" O   GLU B 422 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 416 through 417
      removed outlier: 7.128A  pdb=" N   CYS B 416 " --> pdb=" O   THR C  58 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 432 through 436
    Processing sheet with id=AA8, first strand: chain 'B' and resid 482 through 484
      removed outlier: 4.264A  pdb=" N   LEU B 462 " --> pdb=" O   LYS B 484 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 482 through 484
      removed outlier: 4.264A  pdb=" N   LEU B 462 " --> pdb=" O   LYS B 484 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 539 through 545
      removed outlier: 5.344A  pdb=" N   ASN B 540 " --> pdb=" O   GLU B 557 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   GLU B 557 " --> pdb=" O   ASN B 540 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 582 through 586
    Processing sheet with id=AB3, first strand: chain 'D' and resid 240 through 246
      removed outlier: 5.959A  pdb=" N   GLY D 241 " --> pdb=" O   ASP D 257 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   ASP D 257 " --> pdb=" O   GLY D 241 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 279 through 286
    Processing sheet with id=AB5, first strand: chain 'D' and resid 331 through 334
    Processing sheet with id=AB6, first strand: chain 'D' and resid 337 through 341
    Processing sheet with id=AB7, first strand: chain 'D' and resid 416 through 417
      removed outlier: 7.020A  pdb=" N   CYS D 416 " --> pdb=" O   THR E  58 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'D' and resid 433 through 436
    Processing sheet with id=AB9, first strand: chain 'D' and resid 482 through 484
      removed outlier: 4.759A  pdb=" N   LEU D 462 " --> pdb=" O   LYS D 484 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 482 through 484
      removed outlier: 4.759A  pdb=" N   LEU D 462 " --> pdb=" O   LYS D 484 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 539 through 545
      removed outlier: 5.262A  pdb=" N   ASN D 540 " --> pdb=" O   GLU D 557 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   GLU D 557 " --> pdb=" O   ASN D 540 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 582 through 586
    Processing sheet with id=AC4, first strand: chain 'F' and resid 240 through 246
      removed outlier: 6.008A  pdb=" N   GLY F 241 " --> pdb=" O   ASP F 257 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   ASP F 257 " --> pdb=" O   GLY F 241 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'F' and resid 279 through 286
    Processing sheet with id=AC6, first strand: chain 'F' and resid 331 through 334
    Processing sheet with id=AC7, first strand: chain 'F' and resid 337 through 341
      removed outlier: 3.670A  pdb=" N   ILE F 338 " --> pdb=" O   GLU F 422 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'F' and resid 432 through 436
    Processing sheet with id=AC9, first strand: chain 'F' and resid 482 through 483
    Processing sheet with id=AD1, first strand: chain 'F' and resid 482 through 483
    Processing sheet with id=AD2, first strand: chain 'F' and resid 539 through 545
      removed outlier: 5.427A  pdb=" N   ASN F 540 " --> pdb=" O   GLU F 557 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   GLU F 557 " --> pdb=" O   ASN F 540 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'F' and resid 582 through 586

    615 hydrogen bonds defined for protein.
    1635 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.98

  Time building geometry restraints manager: 3.37 seconds

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

  Histogram of bond lengths:
        1.15 -     1.30: 2092
        1.30 -     1.46: 4085
        1.46 -     1.61: 6810
        1.61 -     1.76: 1
        1.76 -     1.92: 77
  Bond restraints: 13065
  Sorted by residual:
  bond pdb=" CG  ASN A 103 "
       pdb=" OD1 ASN A 103 "
    ideal  model  delta    sigma   weight residual
    1.231  1.150  0.081 1.90e-02 2.77e+03 1.83e+01
  bond pdb=" CG  LYS E  74 "
       pdb=" CD  LYS E  74 "
    ideal  model  delta    sigma   weight residual
    1.520  1.404  0.116 3.00e-02 1.11e+03 1.50e+01
  bond pdb=" CG  ASN A 103 "
       pdb=" ND2 ASN A 103 "
    ideal  model  delta    sigma   weight residual
    1.328  1.247  0.081 2.10e-02 2.27e+03 1.48e+01
  bond pdb=" CB  CYS B 486 "
       pdb=" SG  CYS B 486 "
    ideal  model  delta    sigma   weight residual
    1.808  1.917 -0.109 3.30e-02 9.18e+02 1.10e+01
  bond pdb=" CB  THR C  58 "
       pdb=" CG2 THR C  58 "
    ideal  model  delta    sigma   weight residual
    1.521  1.417  0.104 3.30e-02 9.18e+02 9.85e+00
  ... (remaining 13060 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.98: 17738
        5.98 -    11.96: 60
       11.96 -    17.93: 7
       17.93 -    23.91: 2
       23.91 -    29.89: 1
  Bond angle restraints: 17808
  Sorted by residual:
  angle pdb=" CA  CYS F 486 "
        pdb=" CB  CYS F 486 "
        pdb=" SG  CYS F 486 "
      ideal   model   delta    sigma   weight residual
     114.40  144.29  -29.89 2.30e+00 1.89e-01 1.69e+02
  angle pdb=" CA  CYS F 496 "
        pdb=" CB  CYS F 496 "
        pdb=" SG  CYS F 496 "
      ideal   model   delta    sigma   weight residual
     114.40  134.97  -20.57 2.30e+00 1.89e-01 8.00e+01
  angle pdb=" C   CYS F 496 "
        pdb=" CA  CYS F 496 "
        pdb=" CB  CYS F 496 "
      ideal   model   delta    sigma   weight residual
     110.16  122.15  -11.99 1.66e+00 3.63e-01 5.22e+01
  angle pdb=" CG  LYS E  74 "
        pdb=" CD  LYS E  74 "
        pdb=" CE  LYS E  74 "
      ideal   model   delta    sigma   weight residual
     111.30   95.52   15.78 2.30e+00 1.89e-01 4.71e+01
  angle pdb=" C   CYS F 486 "
        pdb=" CA  CYS F 486 "
        pdb=" CB  CYS F 486 "
      ideal   model   delta    sigma   weight residual
     109.37  121.89  -12.52 1.83e+00 2.99e-01 4.68e+01
  ... (remaining 17803 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 7333
       17.65 -    35.30: 511
       35.30 -    52.95: 78
       52.95 -    70.59: 37
       70.59 -    88.24: 12
  Dihedral angle restraints: 7971
    sinusoidal: 3198
      harmonic: 4773
  Sorted by residual:
  dihedral pdb=" CB  CYS F 486 "
           pdb=" SG  CYS F 486 "
           pdb=" SG  CYS F 496 "
           pdb=" CB  CYS F 496 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -16.56  -69.44     1      1.00e+01 1.00e-02 6.23e+01
  dihedral pdb=" CB  CYS B 486 "
           pdb=" SG  CYS B 486 "
           pdb=" SG  CYS B 496 "
           pdb=" CB  CYS B 496 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   31.72   61.28     1      1.00e+01 1.00e-02 4.99e+01
  dihedral pdb=" C   CYS F 486 "
           pdb=" N   CYS F 486 "
           pdb=" CA  CYS F 486 "
           pdb=" CB  CYS F 486 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.14   16.54     0      2.50e+00 1.60e-01 4.38e+01
  ... (remaining 7968 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.127: 1979
       0.127 -    0.253: 76
       0.253 -    0.380: 4
       0.380 -    0.507: 1
       0.507 -    0.633: 4
  Chirality restraints: 2064
  Sorted by residual:
  chirality pdb=" CB  THR C  58 "
            pdb=" CA  THR C  58 "
            pdb=" OG1 THR C  58 "
            pdb=" CG2 THR C  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    1.92    0.63 2.00e-01 2.50e+01 1.00e+01
  chirality pdb=" CB  ILE E  69 "
            pdb=" CA  ILE E  69 "
            pdb=" CG1 ILE E  69 "
            pdb=" CG2 ILE E  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.06    0.59 2.00e-01 2.50e+01 8.59e+00
  chirality pdb=" CA  CYS F 486 "
            pdb=" N   CYS F 486 "
            pdb=" C   CYS F 486 "
            pdb=" CB  CYS F 486 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.95    0.56 2.00e-01 2.50e+01 7.77e+00
  ... (remaining 2061 not shown)

  Planarity restraints: 2259
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A  63 "    0.073 5.00e-02 4.00e+02   1.08e-01 1.87e+01
        pdb=" N   PRO A  64 "   -0.187 5.00e-02 4.00e+02
        pdb=" CA  PRO A  64 "    0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO A  64 "    0.057 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 103 "    0.020 2.00e-02 2.50e+03   4.23e-02 1.79e+01
        pdb=" CG  ASN A 103 "   -0.073 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 103 "    0.028 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 103 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE E  63 "    0.059 5.00e-02 4.00e+02   8.74e-02 1.22e+01
        pdb=" N   PRO E  64 "   -0.151 5.00e-02 4.00e+02
        pdb=" CA  PRO E  64 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO E  64 "    0.047 5.00e-02 4.00e+02
  ... (remaining 2256 not shown)

  Histogram of nonbonded interaction distances:
        1.78 -     2.40: 39
        2.40 -     3.03: 7364
        3.03 -     3.65: 19511
        3.65 -     4.28: 28279
        4.28 -     4.90: 46720
  Nonbonded interactions: 101913
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG E  41 "
            pdb=" O   TYR F 439 "
     model   vdw
     1.776 3.120
  nonbonded pdb=" ND2 ASN A 103 "
            pdb=" N   LEU B 504 "
     model   vdw
     1.888 3.200
  nonbonded pdb=" OH  TYR B 409 "
            pdb=" CB  SER C 141 "
     model   vdw
     1.972 3.440
  nonbonded pdb=" NH1 ARG B 512 "
            pdb=" OD1 ASN B 514 "
     model   vdw
     2.071 3.120
  nonbonded pdb=" OE1 GLU B 274 "
            pdb=" NH1 ARG B 280 "
     model   vdw
     2.129 3.120
  ... (remaining 101908 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.120
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     28.910
  Find NCS groups from input model:        0.550
  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:             0.000
  Load rotamer database and sin/cos tables:2.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
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      :  0.005   0.116  13083  Z= 0.215
  Angle     :  1.106  29.888  17844  Z= 0.589
  Chirality :  0.064   0.633   2064
  Planarity :  0.006   0.108   2259
  Dihedral  : 13.218  88.242   4815
  Min Nonbonded Distance : 1.776

Molprobity Statistics.
  All-atom Clashscore : 15.37
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  5.25 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.19), residues: 1599
  helix: -0.38 (0.26), residues: 300
  sheet:  0.20 (0.19), residues: 546
  loop : -0.90 (0.21), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP F 447 
 HIS   0.007   0.001   HIS C  47 
 PHE   0.029   0.002   PHE B 502 
 TYR   0.031   0.003   TYR B 470 
 ARG   0.029   0.002   ARG B 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12041 (  577)
  hydrogen bonds       : angle       6.73107 ( 1635)
  SS BOND              : bond        0.01468 (   18)
  SS BOND              : angle       3.71075 (   36)
  covalent geometry    : bond        0.00489 (13065)
  covalent geometry    : angle       1.09439 (17808)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LEU cc_start: 0.9656 (mm) cc_final: 0.9434 (mp)
REVERT: A  110 LEU cc_start: 0.8700 (mm) cc_final: 0.8374 (mm)
REVERT: A  143 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8797 (tm-30)
REVERT: C   30 ASP cc_start: 0.8730 (m-30) cc_final: 0.8506 (m-30)
REVERT: C  106 ASP cc_start: 0.8934 (m-30) cc_final: 0.8654 (m-30)
REVERT: C  156 ASP cc_start: 0.9073 (m-30) cc_final: 0.8829 (m-30)
REVERT: D  584 HIS cc_start: 0.9178 (t70) cc_final: 0.8862 (t-170)
REVERT: E   69 ILE cc_start: 0.8398 (tp) cc_final: 0.8122 (pt)
REVERT: F  302 TYR cc_start: 0.8494 (m-80) cc_final: 0.8049 (m-80)
REVERT: F  366 TRP cc_start: 0.7657 (m100) cc_final: 0.7429 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.2038
  time to fit residues: 45.3676
Evaluate side-chains
  92 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 1.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 134 optimal weight:    6.9990
   chunk 120 optimal weight:    0.0980
   chunk 66 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 64 optimal weight:    7.9990
   chunk 124 optimal weight:    0.6980
   chunk 48 optimal weight:    8.9990
   chunk 75 optimal weight:   50.0000
   chunk 92 optimal weight:    6.9990
   chunk 144 optimal weight:    3.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A  67 HIS
A 103 ASN
A 159 GLN
B 324 GLN
B 461 GLN
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 103 ASN
E  67 HIS
E 103 ASN
E 155 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.076414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.060611 restraints weight = 71804.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.061043 restraints weight = 39690.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.062360 restraints weight = 26246.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.1478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.084  13083  Z= 0.151
  Angle     :  0.675  13.290  17844  Z= 0.348
  Chirality :  0.047   0.365   2064
  Planarity :  0.004   0.049   2259
  Dihedral  :  5.477  65.051   1740
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  2.69 %
    Favored  : 97.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.20), residues: 1599
  helix:  1.35 (0.29), residues: 306
  sheet:  0.70 (0.19), residues: 540
  loop : -0.12 (0.23), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 556 
 HIS   0.011   0.001   HIS E  67 
 PHE   0.008   0.001   PHE B 502 
 TYR   0.016   0.001   TYR B 470 
 ARG   0.006   0.001   ARG F 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04227 (  577)
  hydrogen bonds       : angle       5.64920 ( 1635)
  SS BOND              : bond        0.00497 (   18)
  SS BOND              : angle       1.86638 (   36)
  covalent geometry    : bond        0.00330 (13065)
  covalent geometry    : angle       0.67065 (17808)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 130
  time to evaluate  : 1.389 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8604 (mm-30)
REVERT: A  143 GLU cc_start: 0.9255 (tm-30) cc_final: 0.8929 (tm-30)
REVERT: C   37 THR cc_start: 0.9552 (m) cc_final: 0.9246 (m)
REVERT: C  106 ASP cc_start: 0.8946 (m-30) cc_final: 0.8686 (m-30)
REVERT: C  156 ASP cc_start: 0.9168 (m-30) cc_final: 0.8947 (m-30)
REVERT: D  252 LEU cc_start: 0.9005 (tt) cc_final: 0.8753 (tt)
REVERT: D  584 HIS cc_start: 0.9088 (t70) cc_final: 0.8748 (t-170)
REVERT: E   35 ILE cc_start: 0.9698 (mt) cc_final: 0.9285 (tt)
REVERT: F  302 TYR cc_start: 0.8432 (m-80) cc_final: 0.8076 (m-80)
REVERT: F  366 TRP cc_start: 0.7681 (m100) cc_final: 0.7190 (m100)
  outliers start: 3
  outliers final: 1
  residues processed: 133
  average time/residue: 0.1987
  time to fit residues: 41.5543
Evaluate side-chains
  83 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 1.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 127 optimal weight:    7.9990
   chunk 41 optimal weight:    5.9990
   chunk 132 optimal weight:    0.0970
   chunk 45 optimal weight:    0.9990
   chunk 143 optimal weight:    0.7980
   chunk 119 optimal weight:    0.1980
   chunk 123 optimal weight:    9.9990
   chunk 145 optimal weight:    2.9990
   chunk 83 optimal weight:    0.5980
   chunk 122 optimal weight:   10.0000
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
B 461 GLN
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 160 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.076580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.060615 restraints weight = 71245.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.061058 restraints weight = 39085.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.062447 restraints weight = 25841.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  13083  Z= 0.112
  Angle     :  0.609  12.602  17844  Z= 0.310
  Chirality :  0.044   0.245   2064
  Planarity :  0.004   0.035   2259
  Dihedral  :  5.119  61.479   1740
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.35 %
    Favored  : 97.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.21), residues: 1599
  helix:  1.78 (0.29), residues: 306
  sheet:  0.80 (0.19), residues: 593
  loop :  0.22 (0.25), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 367 
 HIS   0.004   0.001   HIS A  67 
 PHE   0.008   0.001   PHE F 334 
 TYR   0.014   0.001   TYR D 424 
 ARG   0.005   0.000   ARG F 368 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03851 (  577)
  hydrogen bonds       : angle       5.27842 ( 1635)
  SS BOND              : bond        0.00256 (   18)
  SS BOND              : angle       1.89756 (   36)
  covalent geometry    : bond        0.00244 (13065)
  covalent geometry    : angle       0.60399 (17808)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 129
  time to evaluate  : 1.435 
Fit side-chains
REVERT: A  102 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8423 (mm-30)
REVERT: A  110 LEU cc_start: 0.8688 (mm) cc_final: 0.8287 (mm)
REVERT: A  143 GLU cc_start: 0.9237 (tm-30) cc_final: 0.8974 (tm-30)
REVERT: B  461 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8753 (pp30)
REVERT: C   37 THR cc_start: 0.9523 (m) cc_final: 0.9173 (m)
REVERT: C  106 ASP cc_start: 0.8927 (m-30) cc_final: 0.8659 (m-30)
REVERT: C  156 ASP cc_start: 0.9129 (m-30) cc_final: 0.8866 (m-30)
REVERT: D  252 LEU cc_start: 0.8939 (tt) cc_final: 0.8683 (tt)
REVERT: D  584 HIS cc_start: 0.9109 (t70) cc_final: 0.8769 (t-170)
REVERT: E   35 ILE cc_start: 0.9691 (mt) cc_final: 0.9296 (tt)
REVERT: E   76 ASP cc_start: 0.8791 (t0) cc_final: 0.8554 (t0)
REVERT: E   95 LEU cc_start: 0.9491 (mt) cc_final: 0.9271 (mt)
REVERT: F  302 TYR cc_start: 0.8433 (m-80) cc_final: 0.8055 (m-80)
REVERT: F  366 TRP cc_start: 0.7555 (m100) cc_final: 0.7080 (m100)
  outliers start: 2
  outliers final: 0
  residues processed: 131
  average time/residue: 0.2097
  time to fit residues: 42.2347
Evaluate side-chains
  88 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 1.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 146 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 121 optimal weight:    8.9990
   chunk 27 optimal weight:    1.9990
   chunk 86 optimal weight:    9.9990
   chunk 62 optimal weight:    0.8980
   chunk 138 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   chunk 4 optimal weight:    5.9990
   chunk 103 optimal weight:    1.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
B 461 GLN
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  43 ASN
** E  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.074195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.058989 restraints weight = 70607.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.058926 restraints weight = 39493.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.059777 restraints weight = 26762.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13083  Z= 0.138
  Angle     :  0.596  10.163  17844  Z= 0.304
  Chirality :  0.044   0.229   2064
  Planarity :  0.004   0.042   2259
  Dihedral  :  5.103  63.975   1740
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  3.76 %
    Favored  : 96.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.21), residues: 1599
  helix:  1.83 (0.30), residues: 306
  sheet:  0.94 (0.20), residues: 586
  loop :  0.27 (0.25), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 556 
 HIS   0.005   0.001   HIS E 109 
 PHE   0.009   0.001   PHE E 113 
 TYR   0.012   0.001   TYR B 470 
 ARG   0.010   0.001   ARG D 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03684 (  577)
  hydrogen bonds       : angle       5.12631 ( 1635)
  SS BOND              : bond        0.00414 (   18)
  SS BOND              : angle       2.10701 (   36)
  covalent geometry    : bond        0.00304 (13065)
  covalent geometry    : angle       0.58908 (17808)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 1.616 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 ASP cc_start: 0.8987 (m-30) cc_final: 0.8723 (m-30)
REVERT: A  102 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8458 (mm-30)
REVERT: A  110 LEU cc_start: 0.8730 (mm) cc_final: 0.8290 (mm)
REVERT: A  143 GLU cc_start: 0.9284 (tm-30) cc_final: 0.8956 (tm-30)
REVERT: B  461 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8867 (pp30)
REVERT: C   37 THR cc_start: 0.9524 (m) cc_final: 0.9152 (m)
REVERT: C  156 ASP cc_start: 0.9099 (m-30) cc_final: 0.8782 (m-30)
REVERT: D  252 LEU cc_start: 0.8959 (tt) cc_final: 0.8707 (tt)
REVERT: D  584 HIS cc_start: 0.9159 (t70) cc_final: 0.8696 (t-170)
REVERT: E   35 ILE cc_start: 0.9612 (mt) cc_final: 0.9366 (tt)
REVERT: E   76 ASP cc_start: 0.8746 (t0) cc_final: 0.8470 (t0)
REVERT: F  302 TYR cc_start: 0.8631 (m-80) cc_final: 0.8255 (m-80)
REVERT: F  366 TRP cc_start: 0.7781 (m100) cc_final: 0.7317 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 125
  average time/residue: 0.2058
  time to fit residues: 41.0959
Evaluate side-chains
  86 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 1.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 89 optimal weight:    3.9990
   chunk 125 optimal weight:   20.0000
   chunk 22 optimal weight:    9.9990
   chunk 76 optimal weight:    7.9990
   chunk 62 optimal weight:    0.0270
   chunk 136 optimal weight:    0.9980
   chunk 3 optimal weight:   10.0000
   chunk 45 optimal weight:   10.0000
   chunk 48 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    3.2044

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

Flipped N/Q/H residues before XYZ refinement:
** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 489 GLN
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 461 GLN
E  43 ASN
** E  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 103 ASN
F 305 GLN
F 461 GLN
F 478 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.070145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.054811 restraints weight = 72488.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.055648 restraints weight = 48024.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.056456 restraints weight = 24880.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.3368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068  13083  Z= 0.250
  Angle     :  0.726  14.679  17844  Z= 0.373
  Chirality :  0.045   0.250   2064
  Planarity :  0.005   0.075   2259
  Dihedral  :  5.532  70.774   1740
  Min Nonbonded Distance : 1.802

Molprobity Statistics.
  All-atom Clashscore : 14.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.21), residues: 1599
  helix:  1.40 (0.29), residues: 306
  sheet:  0.66 (0.20), residues: 608
  loop :  0.39 (0.26), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 367 
 HIS   0.006   0.002   HIS D 417 
 PHE   0.015   0.002   PHE D 403 
 TYR   0.018   0.002   TYR F 619 
 ARG   0.014   0.001   ARG F 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04164 (  577)
  hydrogen bonds       : angle       5.59192 ( 1635)
  SS BOND              : bond        0.00848 (   18)
  SS BOND              : angle       2.01403 (   36)
  covalent geometry    : bond        0.00523 (13065)
  covalent geometry    : angle       0.72112 (17808)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  632 MET cc_start: 0.5108 (ptt) cc_final: 0.4739 (ptt)
REVERT: C   36 LYS cc_start: 0.9117 (pptt) cc_final: 0.8886 (pptt)
REVERT: C   37 THR cc_start: 0.9568 (m) cc_final: 0.9173 (m)
REVERT: C  106 ASP cc_start: 0.9212 (t0) cc_final: 0.8945 (t0)
REVERT: C  156 ASP cc_start: 0.9020 (m-30) cc_final: 0.8679 (m-30)
REVERT: D  584 HIS cc_start: 0.9221 (t70) cc_final: 0.9006 (t70)
REVERT: E   61 ASP cc_start: 0.8297 (p0) cc_final: 0.8033 (p0)
REVERT: F  366 TRP cc_start: 0.8365 (m100) cc_final: 0.8070 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.2106
  time to fit residues: 34.9979
Evaluate side-chains
  76 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 1.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 114 optimal weight:    0.7980
   chunk 139 optimal weight:    0.8980
   chunk 104 optimal weight:    7.9990
   chunk 117 optimal weight:    3.9990
   chunk 111 optimal weight:    0.9990
   chunk 79 optimal weight:    8.9990
   chunk 141 optimal weight:    0.6980
   chunk 64 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 81 optimal weight:    0.6980
   chunk 144 optimal weight:    0.8980
   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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  43 ASN
** E  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 465 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.072077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.056706 restraints weight = 72985.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.057684 restraints weight = 48181.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.058226 restraints weight = 27832.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.3456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  13083  Z= 0.112
  Angle     :  0.594  11.478  17844  Z= 0.304
  Chirality :  0.044   0.331   2064
  Planarity :  0.004   0.061   2259
  Dihedral  :  5.147  57.313   1740
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.21), residues: 1599
  helix:  1.79 (0.30), residues: 303
  sheet:  0.84 (0.20), residues: 609
  loop :  0.45 (0.26), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 367 
 HIS   0.008   0.001   HIS C 109 
 PHE   0.011   0.001   PHE F 334 
 TYR   0.019   0.001   TYR D 424 
 ARG   0.004   0.000   ARG A  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03703 (  577)
  hydrogen bonds       : angle       5.04585 ( 1635)
  SS BOND              : bond        0.00224 (   18)
  SS BOND              : angle       1.77943 (   36)
  covalent geometry    : bond        0.00238 (13065)
  covalent geometry    : angle       0.58954 (17808)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 1.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 ASP cc_start: 0.8905 (m-30) cc_final: 0.8631 (m-30)
REVERT: A  102 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8376 (mm-30)
REVERT: B  632 MET cc_start: 0.5071 (ptt) cc_final: 0.4357 (ptt)
REVERT: C   30 ASP cc_start: 0.8917 (m-30) cc_final: 0.8712 (m-30)
REVERT: C   36 LYS cc_start: 0.9078 (pptt) cc_final: 0.8817 (pptt)
REVERT: C   37 THR cc_start: 0.9559 (m) cc_final: 0.9186 (m)
REVERT: C  106 ASP cc_start: 0.8842 (t0) cc_final: 0.8445 (t0)
REVERT: C  156 ASP cc_start: 0.8963 (m-30) cc_final: 0.8631 (m-30)
REVERT: D  584 HIS cc_start: 0.9227 (t70) cc_final: 0.9009 (t70)
REVERT: F  366 TRP cc_start: 0.7887 (m100) cc_final: 0.7684 (m100)
REVERT: F  509 MET cc_start: 0.8961 (mpp) cc_final: 0.8584 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.2079
  time to fit residues: 36.1297
Evaluate side-chains
  88 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 1.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 22 optimal weight:   40.0000
   chunk 147 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 130 optimal weight:    0.9990
   chunk 102 optimal weight:    5.9990
   chunk 129 optimal weight:    7.9990
   chunk 46 optimal weight:   10.0000
   chunk 101 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 96 optimal weight:    9.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  77 GLN
C  83 GLN
D 305 GLN
** E  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 103 ASN
F 363 GLN
F 461 GLN
F 567 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.066804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.051551 restraints weight = 77016.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.052050 restraints weight = 50865.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.052784 restraints weight = 28037.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.4606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055  13083  Z= 0.307
  Angle     :  0.809  13.264  17844  Z= 0.418
  Chirality :  0.048   0.389   2064
  Planarity :  0.006   0.102   2259
  Dihedral  :  5.979  79.372   1740
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 20.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.95 %
    Favored  : 97.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.21), residues: 1599
  helix:  1.05 (0.28), residues: 303
  sheet:  0.61 (0.21), residues: 571
  loop :  0.07 (0.25), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D 366 
 HIS   0.016   0.003   HIS F 478 
 PHE   0.032   0.003   PHE D 326 
 TYR   0.024   0.003   TYR F 619 
 ARG   0.008   0.001   ARG E 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04574 (  577)
  hydrogen bonds       : angle       5.89892 ( 1635)
  SS BOND              : bond        0.00474 (   18)
  SS BOND              : angle       2.19584 (   36)
  covalent geometry    : bond        0.00632 (13065)
  covalent geometry    : angle       0.80353 (17808)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 1.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  384 ASP cc_start: 0.8510 (m-30) cc_final: 0.8280 (p0)
REVERT: B  632 MET cc_start: 0.6499 (ptt) cc_final: 0.5936 (ptt)
REVERT: C  106 ASP cc_start: 0.9278 (t0) cc_final: 0.9034 (t0)
REVERT: C  156 ASP cc_start: 0.9072 (m-30) cc_final: 0.8798 (m-30)
REVERT: D  600 ASP cc_start: 0.8643 (p0) cc_final: 0.8443 (t70)
REVERT: E   61 ASP cc_start: 0.8523 (p0) cc_final: 0.8301 (p0)
REVERT: F  366 TRP cc_start: 0.8592 (m100) cc_final: 0.8318 (m100)
REVERT: F  384 ASP cc_start: 0.8395 (m-30) cc_final: 0.7910 (p0)
REVERT: F  632 MET cc_start: 0.2745 (ttp) cc_final: 0.2493 (tmm)
  outliers start: 1
  outliers final: 1
  residues processed: 95
  average time/residue: 0.2123
  time to fit residues: 31.9743
Evaluate side-chains
  69 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 1.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 89 optimal weight:    6.9990
   chunk 87 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 157 optimal weight:    9.9990
   chunk 120 optimal weight:    0.0370
   chunk 58 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9980
   overall best weight:    1.0060

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

Flipped N/Q/H residues before XYZ refinement:
B 461 GLN
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  77 GLN
** E  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 349 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.068917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.053539 restraints weight = 75517.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.052563 restraints weight = 42569.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.053505 restraints weight = 34654.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.4538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13083  Z= 0.127
  Angle     :  0.631  12.251  17844  Z= 0.325
  Chirality :  0.045   0.294   2064
  Planarity :  0.005   0.130   2259
  Dihedral  :  5.453  69.226   1740
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.94 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.22), residues: 1599
  helix:  1.55 (0.30), residues: 303
  sheet:  0.67 (0.21), residues: 597
  loop :  0.32 (0.26), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 447 
 HIS   0.004   0.001   HIS B 349 
 PHE   0.020   0.002   PHE F 334 
 TYR   0.037   0.001   TYR C  82 
 ARG   0.012   0.001   ARG D 446 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03843 (  577)
  hydrogen bonds       : angle       5.33560 ( 1635)
  SS BOND              : bond        0.00200 (   18)
  SS BOND              : angle       1.92753 (   36)
  covalent geometry    : bond        0.00278 (13065)
  covalent geometry    : angle       0.62559 (17808)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 106
  time to evaluate  : 1.634 
Fit side-chains
REVERT: A  102 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8406 (mm-30)
REVERT: B  384 ASP cc_start: 0.8572 (m-30) cc_final: 0.8314 (p0)
REVERT: B  461 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8542 (pp30)
REVERT: C   30 ASP cc_start: 0.9159 (m-30) cc_final: 0.8839 (m-30)
REVERT: C   36 LYS cc_start: 0.9025 (pptt) cc_final: 0.8732 (pptt)
REVERT: C   37 THR cc_start: 0.9576 (m) cc_final: 0.9211 (m)
REVERT: C  106 ASP cc_start: 0.9276 (t0) cc_final: 0.8910 (t0)
REVERT: C  156 ASP cc_start: 0.9076 (m-30) cc_final: 0.8803 (m-30)
REVERT: D  584 HIS cc_start: 0.9482 (t70) cc_final: 0.9260 (t70)
REVERT: E   61 ASP cc_start: 0.8362 (p0) cc_final: 0.8115 (p0)
REVERT: E   75 MET cc_start: 0.8987 (ptp) cc_final: 0.8537 (ptp)
REVERT: F  366 TRP cc_start: 0.8160 (m100) cc_final: 0.7849 (m100)
  outliers start: 2
  outliers final: 0
  residues processed: 108
  average time/residue: 0.2044
  time to fit residues: 35.6555
Evaluate side-chains
  71 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 1.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 21 optimal weight:    9.9990
   chunk 73 optimal weight:    6.9990
   chunk 148 optimal weight:    5.9990
   chunk 6 optimal weight:    0.7980
   chunk 118 optimal weight:    5.9990
   chunk 147 optimal weight:    0.9980
   chunk 46 optimal weight:    6.9990
   chunk 102 optimal weight:    0.7980
   chunk 76 optimal weight:    6.9990
   chunk 143 optimal weight:    0.9980
   overall best weight:    1.9182

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

Flipped N/Q/H residues before XYZ refinement:
** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  77 GLN
** E  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 103 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.067752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.050857 restraints weight = 75210.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.052058 restraints weight = 48287.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.052666 restraints weight = 28706.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.4779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13083  Z= 0.164
  Angle     :  0.635  11.395  17844  Z= 0.329
  Chirality :  0.045   0.326   2064
  Planarity :  0.005   0.118   2259
  Dihedral  :  5.409  71.886   1740
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 13.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.54 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.22), residues: 1599
  helix:  1.60 (0.30), residues: 303
  sheet:  0.64 (0.21), residues: 597
  loop :  0.33 (0.26), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 556 
 HIS   0.006   0.001   HIS F 349 
 PHE   0.010   0.002   PHE F 334 
 TYR   0.034   0.002   TYR C  82 
 ARG   0.007   0.001   ARG D 446 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03786 (  577)
  hydrogen bonds       : angle       5.33404 ( 1635)
  SS BOND              : bond        0.00243 (   18)
  SS BOND              : angle       1.90219 (   36)
  covalent geometry    : bond        0.00349 (13065)
  covalent geometry    : angle       0.62938 (17808)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 1.412 
Fit side-chains
REVERT: A  102 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8412 (mm-30)
REVERT: B  384 ASP cc_start: 0.8696 (m-30) cc_final: 0.8408 (p0)
REVERT: C   30 ASP cc_start: 0.9177 (m-30) cc_final: 0.8834 (m-30)
REVERT: C   36 LYS cc_start: 0.9081 (pptt) cc_final: 0.8836 (pptt)
REVERT: C   37 THR cc_start: 0.9596 (m) cc_final: 0.9248 (m)
REVERT: C  106 ASP cc_start: 0.9348 (t0) cc_final: 0.9044 (t0)
REVERT: C  156 ASP cc_start: 0.9117 (m-30) cc_final: 0.8779 (m-30)
REVERT: D  584 HIS cc_start: 0.9484 (t70) cc_final: 0.9267 (t70)
REVERT: F  366 TRP cc_start: 0.8214 (m100) cc_final: 0.7829 (m100)
REVERT: F  384 ASP cc_start: 0.8354 (m-30) cc_final: 0.7769 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 106
  average time/residue: 0.2008
  time to fit residues: 33.5552
Evaluate side-chains
  68 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 1.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 133 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 96 optimal weight:   10.0000
   chunk 60 optimal weight:    0.8980
   chunk 88 optimal weight:    4.9990
   chunk 100 optimal weight:    9.9990
   chunk 55 optimal weight:    3.9990
   chunk 19 optimal weight:   20.0000
   chunk 126 optimal weight:    0.0970
   chunk 46 optimal weight:    5.9990
   chunk 53 optimal weight:    8.9990
   overall best weight:    2.1982

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

Flipped N/Q/H residues before XYZ refinement:
** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 349 HIS
** E  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 103 ASN
** F 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.066966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.052327 restraints weight = 75609.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.051291 restraints weight = 47876.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.052060 restraints weight = 32253.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.5144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13083  Z= 0.176
  Angle     :  0.662  11.687  17844  Z= 0.342
  Chirality :  0.045   0.314   2064
  Planarity :  0.005   0.109   2259
  Dihedral  :  5.439  71.674   1740
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 14.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.27 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.22), residues: 1599
  helix:  1.38 (0.30), residues: 300
  sheet:  0.64 (0.21), residues: 594
  loop :  0.33 (0.26), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 556 
 HIS   0.006   0.002   HIS F 478 
 PHE   0.020   0.002   PHE F 334 
 TYR   0.032   0.002   TYR C  82 
 ARG   0.010   0.001   ARG D 446 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03914 (  577)
  hydrogen bonds       : angle       5.50878 ( 1635)
  SS BOND              : bond        0.00233 (   18)
  SS BOND              : angle       1.85005 (   36)
  covalent geometry    : bond        0.00376 (13065)
  covalent geometry    : angle       0.65694 (17808)

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

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

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3198 Ramachandran restraints generated.
    1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 1.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 LEU cc_start: 0.8844 (mt) cc_final: 0.8580 (mt)
REVERT: A  102 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8469 (mm-30)
REVERT: C   30 ASP cc_start: 0.9174 (m-30) cc_final: 0.8824 (m-30)
REVERT: C   36 LYS cc_start: 0.9025 (pptt) cc_final: 0.8716 (pptt)
REVERT: C   37 THR cc_start: 0.9574 (m) cc_final: 0.9219 (m)
REVERT: C  106 ASP cc_start: 0.9298 (t0) cc_final: 0.9018 (t0)
REVERT: C  156 ASP cc_start: 0.9161 (m-30) cc_final: 0.8860 (m-30)
REVERT: D  584 HIS cc_start: 0.9512 (t70) cc_final: 0.9288 (t70)
REVERT: F  366 TRP cc_start: 0.8587 (m100) cc_final: 0.8205 (m100)
REVERT: F  384 ASP cc_start: 0.8409 (m-30) cc_final: 0.7879 (p0)
REVERT: F  632 MET cc_start: 0.3975 (tmm) cc_final: 0.3634 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 101
  average time/residue: 0.2054
  time to fit residues: 32.8053
Evaluate side-chains
  72 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 1.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 132 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 112 optimal weight:    0.8980
   chunk 60 optimal weight:    7.9990
   chunk 155 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9980
   chunk 142 optimal weight:    4.9990
   chunk 154 optimal weight:    8.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  77 GLN
** E  67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.067666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.052026 restraints weight = 73709.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.052864 restraints weight = 50181.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.053440 restraints weight = 26115.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.5216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13083  Z= 0.124
  Angle     :  0.619  11.214  17844  Z= 0.318
  Chirality :  0.045   0.299   2064
  Planarity :  0.005   0.093   2259
  Dihedral  :  5.213  66.951   1740
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.00 %
    Favored  : 99.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.22), residues: 1599
  helix:  1.58 (0.30), residues: 300
  sheet:  0.71 (0.21), residues: 594
  loop :  0.39 (0.26), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 447 
 HIS   0.006   0.001   HIS F 349 
 PHE   0.014   0.001   PHE F 334 
 TYR   0.027   0.001   TYR C  82 
 ARG   0.009   0.001   ARG D 446 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03651 (  577)
  hydrogen bonds       : angle       5.23673 ( 1635)
  SS BOND              : bond        0.00205 (   18)
  SS BOND              : angle       1.96868 (   36)
  covalent geometry    : bond        0.00272 (13065)
  covalent geometry    : angle       0.61280 (17808)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3414.81 seconds
wall clock time: 61 minutes 9.42 seconds (3669.42 seconds total)