Starting phenix.real_space_refine
on Tue Feb  3 20:49:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kvf_62592/02_2026/9kvf_62592.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kvf_62592/02_2026/9kvf_62592.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kvf_62592/02_2026/9kvf_62592.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kvf_62592/02_2026/9kvf_62592.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kvf_62592/02_2026/9kvf_62592.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kvf_62592/02_2026/9kvf_62592.map"
  }
  resolution = 3.0
  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=   0.001 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    4341      2.51       5
     N    1170      2.21       5
     O    1267      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6805
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 749
          Classifications: {'peptide': 109}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 6, 'TRANS': 102}
          Unresolved non-hydrogen bonds: 71
          Unresolved non-hydrogen angles: 87
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'ARG:plan': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 37
    Chain: "G"
      Number of atoms: 1948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 265, 1948
          Classifications: {'peptide': 265}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PTRANS': 18, 'TRANS': 246}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 157
          Unresolved non-hydrogen angles: 194
          Unresolved non-hydrogen dihedrals: 128
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 7, 'TYR:plan': 2, 'PHE:plan': 1, 'ASP:plan': 6, 'GLN:plan1': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 92
    Chain: "F"
      Number of atoms: 934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 934
          Classifications: {'peptide': 128}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 2, 'TRANS': 125}
          Unresolved non-hydrogen bonds: 68
          Unresolved non-hydrogen angles: 81
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 36
    Chain: "E"
      Number of atoms: 775
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 775
          Classifications: {'peptide': 109}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 7, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 19
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "B"
      Number of atoms: 812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 812
          Classifications: {'peptide': 119}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 4, 'TRANS': 114}
          Unresolved non-hydrogen bonds: 105
          Unresolved non-hydrogen angles: 130
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 5, 'PHE:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 61
    Chain: "C"
      Number of atoms: 830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 830
          Classifications: {'peptide': 118}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 2, 'TRANS': 115}
          Unresolved non-hydrogen bonds: 88
          Unresolved non-hydrogen angles: 110
          Unresolved non-hydrogen dihedrals: 69
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 38
    Chain: "D"
      Number of atoms: 757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 757
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 98}
          Unresolved non-hydrogen bonds: 65
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 25
  Time building chain proxies: 1.72, per 1000 atoms: 0.25
  Number of scatterers: 6805
  At special positions: 0
  Unit cell: (79.95, 145.6, 98.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      27     16.00
     O    1267      8.00
     N    1170      7.00
     C    4341      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  91 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G 336 " - pdb=" SG  CYS G 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 379 " - pdb=" SG  CYS G 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G 391 " - pdb=" SG  CYS G 525 " distance=2.02
    Simple disulfide: pdb=" SG  CYS G 480 " - pdb=" SG  CYS G 488 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  88 " distance=2.04

  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: 0.65
  Conformation dependent library (CDL) restraints added in 252.4 milliseconds
  

  1878 Ramachandran restraints generated.
    939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1722

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 21 sheets defined
      7.9% alpha, 38.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'G' and resid 338 through 343
    Processing helix  chain 'G' and resid 349 through 353
      removed outlier: 3.863A  pdb=" N   TRP G 353 " --> pdb=" O   VAL G 350 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 365 through 370
    Processing helix  chain 'G' and resid 405 through 408
      removed outlier: 3.989A  pdb=" N   SER G 408 " --> pdb=" O   ASN G 405 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 405 through 408'
    Processing helix  chain 'G' and resid 417 through 422
    Processing helix  chain 'G' and resid 438 through 443
      removed outlier: 3.536A  pdb=" N   SER G 443 " --> pdb=" O   ASN G 439 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 502 through 505
    Processing helix  chain 'F' and resid 87 through 91
      removed outlier: 3.606A  pdb=" N   THR F  91 " --> pdb=" O   GLU F  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.811A  pdb=" N   TYR E  32 " --> pdb=" O   ILE E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 80 through 84
      removed outlier: 3.935A  pdb=" N   GLU E  84 " --> pdb=" O   PRO E  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 32
      removed outlier: 3.794A  pdb=" N   ASP B  31 " --> pdb=" O   THR B  28 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   TYR B  32 " --> pdb=" O   PHE B  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 28 through 32'
    Processing helix  chain 'B' and resid 87 through 91
      removed outlier: 3.507A  pdb=" N   THR B  91 " --> pdb=" O   ALA B  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 30
      No H-bonds generated for 'chain 'C' and resid 28 through 30'
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 3.560A  pdb=" N   THR C  91 " --> pdb=" O   ALA C  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 79 through 83
      removed outlier: 4.025A  pdb=" N   PHE D  83 " --> pdb=" O   PRO D  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6
    Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 10
      removed outlier: 6.479A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 10
    Processing sheet with id=AA4, first strand: chain 'G' and resid 325 through 328
      removed outlier: 5.452A  pdb=" N   ASP G 574 " --> pdb=" O   ILE G 587 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ALA G 575 " --> pdb=" O   GLY G 566 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'G' and resid 354 through 358
    Processing sheet with id=AA6, first strand: chain 'G' and resid 361 through 362
      removed outlier: 6.368A  pdb=" N   CYS G 361 " --> pdb=" O   CYS G 525 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 452 through 454
    Processing sheet with id=AA8, first strand: chain 'G' and resid 473 through 474
    Processing sheet with id=AA9, first strand: chain 'F' and resid 3 through 7
      removed outlier: 3.738A  pdb=" N   LEU F  81 " --> pdb=" O   LEU F  20 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR F  78 " --> pdb=" O   ASP F  73 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 11 through 12
      removed outlier: 6.783A  pdb=" N   MET F  34 " --> pdb=" O   VAL F  50 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   VAL F  50 " --> pdb=" O   MET F  34 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   TRP F  36 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ALA F  40 " --> pdb=" O   GLY F  44 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   GLY F  44 " --> pdb=" O   ALA F  40 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 12
      removed outlier: 6.615A  pdb=" N   VAL E  10 " --> pdb=" O   THR E 108 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   GLN E  38 " --> pdb=" O   LEU E  47 " (cutoff:3.500A)
      removed outlier: 5.648A  pdb=" N   LEU E  47 " --> pdb=" O   GLN E  38 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 9 through 12
      removed outlier: 6.615A  pdb=" N   VAL E  10 " --> pdb=" O   THR E 108 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ALA E  98 " --> pdb=" O   ASP E  93 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 17 through 23
      removed outlier: 3.622A  pdb=" N   SER E  71 " --> pdb=" O   SER E  68 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 17 through 22
    Processing sheet with id=AB6, first strand: chain 'B' and resid 58 through 60
      removed outlier: 6.596A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   GLY B  50 " --> pdb=" O   LEU B  34 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   LEU B  34 " --> pdb=" O   GLY B  50 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 3 through 6
    Processing sheet with id=AB8, first strand: chain 'C' and resid 58 through 60
      removed outlier: 6.614A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   VAL C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   MET C  34 " --> pdb=" O   VAL C  50 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 58 through 60
      removed outlier: 6.614A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   VAL C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   MET C  34 " --> pdb=" O   VAL C  50 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 4 through 7
    Processing sheet with id=AC2, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.882A  pdb=" N   LEU D  11 " --> pdb=" O   ASP D 105 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   TRP D  35 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.882A  pdb=" N   LEU D  11 " --> pdb=" O   ASP D 105 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   THR D  97 " --> pdb=" O   GLN D  90 " (cutoff:3.500A)

    254 hydrogen bonds defined for protein.
    633 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.96

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2231
        1.34 -     1.46: 1863
        1.46 -     1.58: 2858
        1.58 -     1.70: 0
        1.70 -     1.82: 33
  Bond restraints: 6985
  Sorted by residual:
  bond pdb=" N   PRO G 507 "
       pdb=" CD  PRO G 507 "
    ideal  model  delta    sigma   weight residual
    1.473  1.576 -0.103 1.40e-02 5.10e+03 5.37e+01
  bond pdb=" C   LEU C  11 "
       pdb=" N   VAL C  12 "
    ideal  model  delta    sigma   weight residual
    1.332  1.309  0.023 5.60e-03 3.19e+04 1.71e+01
  bond pdb=" CA  SER D  31 "
       pdb=" CB  SER D  31 "
    ideal  model  delta    sigma   weight residual
    1.530  1.491  0.039 1.54e-02 4.22e+03 6.33e+00
  bond pdb=" N   ILE D  29 "
       pdb=" CA  ILE D  29 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.25e-02 6.40e+03 5.38e+00
  bond pdb=" N   SER D  31 "
       pdb=" CA  SER D  31 "
    ideal  model  delta    sigma   weight residual
    1.456  1.484 -0.028 1.22e-02 6.72e+03 5.14e+00
  ... (remaining 6980 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 9177
        1.57 -     3.14: 323
        3.14 -     4.70: 49
        4.70 -     6.27: 14
        6.27 -     7.84: 3
  Bond angle restraints: 9566
  Sorted by residual:
  angle pdb=" C   ASN D  30 "
        pdb=" CA  ASN D  30 "
        pdb=" CB  ASN D  30 "
      ideal   model   delta    sigma   weight residual
     117.23  110.75    6.48 1.36e+00 5.41e-01 2.27e+01
  angle pdb=" N   VAL G 341 "
        pdb=" CA  VAL G 341 "
        pdb=" C   VAL G 341 "
      ideal   model   delta    sigma   weight residual
     112.96  108.29    4.67 1.00e+00 1.00e+00 2.18e+01
  angle pdb=" C   GLY F 121 "
        pdb=" N   VAL F 122 "
        pdb=" CA  VAL F 122 "
      ideal   model   delta    sigma   weight residual
     123.19  117.53    5.66 1.24e+00 6.50e-01 2.08e+01
  angle pdb=" C   TRP C  47 "
        pdb=" N   VAL C  48 "
        pdb=" CA  VAL C  48 "
      ideal   model   delta    sigma   weight residual
     123.16  118.49    4.67 1.06e+00 8.90e-01 1.94e+01
  angle pdb=" C   THR G 572 "
        pdb=" N   THR G 573 "
        pdb=" CA  THR G 573 "
      ideal   model   delta    sigma   weight residual
     123.23  117.38    5.85 1.57e+00 4.06e-01 1.39e+01
  ... (remaining 9561 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 3721
       17.87 -    35.74: 233
       35.74 -    53.60: 34
       53.60 -    71.47: 8
       71.47 -    89.34: 2
  Dihedral angle restraints: 3998
    sinusoidal: 1277
      harmonic: 2721
  Sorted by residual:
  dihedral pdb=" CA  THR F 111 "
           pdb=" C   THR F 111 "
           pdb=" N   GLU F 112 "
           pdb=" CA  GLU F 112 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.53  -21.47     0      5.00e+00 4.00e-02 1.84e+01
  dihedral pdb=" CB  CYS G 391 "
           pdb=" SG  CYS G 391 "
           pdb=" SG  CYS G 525 "
           pdb=" CB  CYS G 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  126.77  -33.77     1      1.00e+01 1.00e-02 1.62e+01
  dihedral pdb=" CA  ARG B 105 "
           pdb=" C   ARG B 105 "
           pdb=" N   PRO B 106 "
           pdb=" CA  PRO B 106 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.98   20.02     0      5.00e+00 4.00e-02 1.60e+01
  ... (remaining 3995 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 720
       0.042 -    0.083: 236
       0.083 -    0.125: 81
       0.125 -    0.166: 14
       0.166 -    0.208: 4
  Chirality restraints: 1055
  Sorted by residual:
  chirality pdb=" CB  ILE B  70 "
            pdb=" CA  ILE B  70 "
            pdb=" CG1 ILE B  70 "
            pdb=" CG2 ILE B  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  ILE D  29 "
            pdb=" N   ILE D  29 "
            pdb=" C   ILE D  29 "
            pdb=" CB  ILE D  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CA  GLN F 120 "
            pdb=" N   GLN F 120 "
            pdb=" C   GLN F 120 "
            pdb=" CB  GLN F 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.68e-01
  ... (remaining 1052 not shown)

  Planarity restraints: 1260
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C  12 "    0.015 2.00e-02 2.50e+03   3.09e-02 9.55e+00
        pdb=" C   VAL C  12 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   VAL C  12 "    0.020 2.00e-02 2.50e+03
        pdb=" N   LYS C  13 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C  11 "   -0.013 2.00e-02 2.50e+03   2.80e-02 7.84e+00
        pdb=" C   LEU C  11 "    0.048 2.00e-02 2.50e+03
        pdb=" O   LEU C  11 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   VAL C  12 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  53 "    0.015 2.00e-02 2.50e+03   1.36e-02 4.65e+00
        pdb=" CG  TRP B  53 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  53 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  53 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  53 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  53 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  53 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  53 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  53 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  53 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1257 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 447
        2.73 -     3.27: 6339
        3.27 -     3.82: 10834
        3.82 -     4.36: 13055
        4.36 -     4.90: 23537
  Nonbonded interactions: 54212
  Sorted by model distance:
  nonbonded pdb=" O   SER A   7 "
            pdb=" OG1 THR A 106 "
     model   vdw
     2.188 3.040
  nonbonded pdb=" O   TYR E  32 "
            pdb=" NZ  LYS E  67 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" O   ASN F  52 "
            pdb=" NH1 ARG F  72 "
     model   vdw
     2.226 3.120
  nonbonded pdb=" OD2 ASP G 398 "
            pdb=" OH  TYR G 423 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   PHE F  29 "
            pdb=" NH2 ARG F  72 "
     model   vdw
     2.273 3.120
  ... (remaining 54207 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.210
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     7.280
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6925
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   0.103   6995  Z= 0.276
  Angle     :  0.723   7.839   9586  Z= 0.432
  Chirality :  0.047   0.208   1055
  Planarity :  0.005   0.046   1260
  Dihedral  : 12.144  89.340   2246
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.41 (0.24), residues: 939
  helix: -4.84 (0.24), residues: 31
  sheet: -1.40 (0.26), residues: 361
  loop : -2.82 (0.22), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G 328 
 TYR   0.018   0.002   TYR A  50 
 PHE   0.017   0.002   PHE A   4 
 TRP   0.037   0.002   TRP B  53 
 HIS   0.003   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00550 ( 6985)
  covalent geometry    : angle       0.72154 ( 9566)
  SS BOND              : bond        0.00549 (   10)
  SS BOND              : angle       1.25434 (   20)
  hydrogen bonds       : bond        0.13863 (  234)
  hydrogen bonds       : angle       8.57691 (  633)

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

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

  1878 Ramachandran restraints generated.
    939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1878 Ramachandran restraints generated.
    939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.244 
Fit side-chains
REVERT: G  343 ASN cc_start: 0.7430 (t0) cc_final: 0.7172 (t0)
REVERT: G  424 LYS cc_start: 0.8014 (tptm) cc_final: 0.7804 (tptt)
REVERT: G  519 HIS cc_start: 0.5990 (m-70) cc_final: 0.5785 (m-70)
REVERT: F   34 MET cc_start: 0.7695 (mmm) cc_final: 0.7215 (mmt)
REVERT: E   87 TYR cc_start: 0.8005 (m-80) cc_final: 0.7706 (m-80)
REVERT: D    4 MET cc_start: 0.7071 (mmm) cc_final: 0.6638 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.2551
  time to fit residues: 33.7546
Evaluate side-chains
  109 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0770
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.5740

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
** G 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 405 ASN
G 422 ASN
G 448 ASN
G 544 ASN
E   6 GLN
E  35 ASN
E  39 GLN
** E  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  54 ASN
C  39 GLN
D   6 GLN
D  38 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.134691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.115630 restraints weight = 9724.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 2.04
r_work: 0.3393 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.1524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6995  Z= 0.158
  Angle     :  0.585   5.692   9586  Z= 0.314
  Chirality :  0.045   0.155   1055
  Planarity :  0.005   0.043   1260
  Dihedral  :  5.143  32.599   1037
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 11.17 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.35 (0.26), residues: 939
  helix: -4.29 (0.42), residues: 31
  sheet: -0.87 (0.27), residues: 344
  loop : -1.91 (0.25), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  72 
 TYR   0.018   0.002   TYR D  49 
 PHE   0.018   0.002   PHE B  93 
 TRP   0.020   0.002   TRP B  53 
 HIS   0.004   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 6985)
  covalent geometry    : angle       0.58485 ( 9566)
  SS BOND              : bond        0.00392 (   10)
  SS BOND              : angle       0.74376 (   20)
  hydrogen bonds       : bond        0.03456 (  234)
  hydrogen bonds       : angle       6.54343 (  633)

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

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

  1878 Ramachandran restraints generated.
    939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1878 Ramachandran restraints generated.
    939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A   31 SER cc_start: 0.7438 (m) cc_final: 0.7235 (t)
REVERT: G  343 ASN cc_start: 0.8076 (t0) cc_final: 0.7798 (t0)
REVERT: G  442 ASP cc_start: 0.7869 (m-30) cc_final: 0.7582 (m-30)
REVERT: G  519 HIS cc_start: 0.7239 (m-70) cc_final: 0.6965 (m-70)
REVERT: D    4 MET cc_start: 0.7677 (mmm) cc_final: 0.7109 (mtp)
REVERT: D    6 GLN cc_start: 0.7290 (mt0) cc_final: 0.7042 (mt0)
  outliers start: 11
  outliers final: 5
  residues processed: 110
  average time/residue: 0.2069
  time to fit residues: 25.5926
Evaluate side-chains
  111 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 106
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  551 VAL
Chi-restraints excluded: chain G residue  558 LYS
Chi-restraints excluded: chain F residue    7 SER
Chi-restraints excluded: chain F residue  114 SER
Chi-restraints excluded: chain E residue   89 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 59 optimal weight:    0.0000
   chunk 87 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.8988

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

Flipped N/Q/H residues before XYZ refinement:
A  39 GLN
G 334 ASN
G 450 ASN
G 544 ASN
E  39 GLN
B  39 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.131345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.112626 restraints weight = 9734.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 2.00
r_work: 0.3363 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3221 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   6995  Z= 0.219
  Angle     :  0.614   6.689   9586  Z= 0.330
  Chirality :  0.046   0.161   1055
  Planarity :  0.005   0.045   1260
  Dihedral  :  5.306  32.272   1037
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 12.32 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.96 (0.27), residues: 939
  helix: -4.08 (0.50), residues: 31
  sheet: -0.63 (0.27), residues: 356
  loop : -1.62 (0.26), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 100 
 TYR   0.019   0.002   TYR A  50 
 PHE   0.016   0.002   PHE B  93 
 TRP   0.025   0.002   TRP B  53 
 HIS   0.004   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 6985)
  covalent geometry    : angle       0.61298 ( 9566)
  SS BOND              : bond        0.00522 (   10)
  SS BOND              : angle       0.95894 (   20)
  hydrogen bonds       : bond        0.03722 (  234)
  hydrogen bonds       : angle       6.35621 (  633)

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

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

  1878 Ramachandran restraints generated.
    939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1878 Ramachandran restraints generated.
    939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.177 
Fit side-chains
REVERT: G  343 ASN cc_start: 0.8289 (t0) cc_final: 0.8027 (t0)
REVERT: G  439 ASN cc_start: 0.8439 (t0) cc_final: 0.7833 (t160)
REVERT: G  442 ASP cc_start: 0.7928 (m-30) cc_final: 0.7666 (m-30)
REVERT: D    4 MET cc_start: 0.7742 (mmm) cc_final: 0.7263 (mtp)
  outliers start: 23
  outliers final: 13
  residues processed: 121
  average time/residue: 0.1999
  time to fit residues: 27.1492
Evaluate side-chains
  118 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  514 SER
Chi-restraints excluded: chain G residue  551 VAL
Chi-restraints excluded: chain G residue  588 THR
Chi-restraints excluded: chain F residue    7 SER
Chi-restraints excluded: chain F residue  114 SER
Chi-restraints excluded: chain E residue   23 THR
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   62 ARG
Chi-restraints excluded: chain E residue   89 CYS
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain D residue   75 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 30 optimal weight:    0.4980
   chunk 20 optimal weight:    0.8980
   chunk 59 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 85 optimal weight:    0.0870
   chunk 68 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 45 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
G 334 ASN
G 422 ASN
G 437 ASN
G 448 ASN
G 542 ASN
G 544 ASN
** F  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN
D   6 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.132256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.113526 restraints weight = 9821.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.01
r_work: 0.3378 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.2519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6995  Z= 0.163
  Angle     :  0.575   6.628   9586  Z= 0.304
  Chirality :  0.045   0.170   1055
  Planarity :  0.005   0.047   1260
  Dihedral  :  5.005  29.776   1037
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 14.78 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.69 (0.27), residues: 939
  helix: -4.03 (0.50), residues: 31
  sheet: -0.39 (0.27), residues: 352
  loop : -1.46 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 100 
 TYR   0.018   0.002   TYR D  49 
 PHE   0.023   0.002   PHE B  29 
 TRP   0.015   0.002   TRP B  53 
 HIS   0.004   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 6985)
  covalent geometry    : angle       0.57466 ( 9566)
  SS BOND              : bond        0.00425 (   10)
  SS BOND              : angle       0.75460 (   20)
  hydrogen bonds       : bond        0.03268 (  234)
  hydrogen bonds       : angle       6.07515 (  633)

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

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

  1878 Ramachandran restraints generated.
    939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1878 Ramachandran restraints generated.
    939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.174 
Fit side-chains
REVERT: G  343 ASN cc_start: 0.8266 (t0) cc_final: 0.7982 (t0)
REVERT: G  442 ASP cc_start: 0.7943 (m-30) cc_final: 0.7692 (m-30)
REVERT: G  443 SER cc_start: 0.7996 (p) cc_final: 0.7704 (p)
REVERT: D    4 MET cc_start: 0.7766 (mmm) cc_final: 0.7249 (mtp)
REVERT: D   32 TYR cc_start: 0.8233 (m-80) cc_final: 0.8011 (m-80)
  outliers start: 18
  outliers final: 14
  residues processed: 110
  average time/residue: 0.2063
  time to fit residues: 25.2758
Evaluate side-chains
  117 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  452 LEU
Chi-restraints excluded: chain G residue  549 THR
Chi-restraints excluded: chain G residue  551 VAL
Chi-restraints excluded: chain G residue  553 THR
Chi-restraints excluded: chain G residue  588 THR
Chi-restraints excluded: chain F residue    7 SER
Chi-restraints excluded: chain F residue  114 SER
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   62 ARG
Chi-restraints excluded: chain E residue   89 CYS
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain D residue   75 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0270
   chunk 53 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 81 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.1844

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

Flipped N/Q/H residues before XYZ refinement:
G 334 ASN
G 354 ASN
** G 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.130827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.112091 restraints weight = 9818.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 1.99
r_work: 0.3354 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.076   6995  Z= 0.271
  Angle     :  0.657   7.326   9586  Z= 0.348
  Chirality :  0.047   0.161   1055
  Planarity :  0.005   0.068   1260
  Dihedral  :  5.408  30.782   1037
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 15.27 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.72 (0.27), residues: 939
  helix: -4.09 (0.45), residues: 31
  sheet: -0.46 (0.27), residues: 358
  loop : -1.45 (0.27), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 100 
 TYR   0.024   0.002   TYR A  50 
 PHE   0.020   0.002   PHE B  93 
 TRP   0.020   0.003   TRP E  36 
 HIS   0.004   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00628 ( 6985)
  covalent geometry    : angle       0.65617 ( 9566)
  SS BOND              : bond        0.00656 (   10)
  SS BOND              : angle       1.06093 (   20)
  hydrogen bonds       : bond        0.03861 (  234)
  hydrogen bonds       : angle       6.35691 (  633)

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

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

  1878 Ramachandran restraints generated.
    939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1878 Ramachandran restraints generated.
    939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 114
  time to evaluate  : 0.243 
Fit side-chains
REVERT: G  343 ASN cc_start: 0.8266 (t0) cc_final: 0.7997 (t0)
REVERT: G  439 ASN cc_start: 0.8417 (t0) cc_final: 0.7899 (t160)
REVERT: G  442 ASP cc_start: 0.7980 (m-30) cc_final: 0.7693 (m-30)
REVERT: G  443 SER cc_start: 0.7923 (p) cc_final: 0.7474 (p)
REVERT: F   34 MET cc_start: 0.8206 (mmm) cc_final: 0.7799 (mmt)
REVERT: C  107 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.7090 (mtp)
REVERT: D    4 MET cc_start: 0.7774 (mmm) cc_final: 0.7272 (mtp)
  outliers start: 25
  outliers final: 18
  residues processed: 124
  average time/residue: 0.1923
  time to fit residues: 26.9564
Evaluate side-chains
  130 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  452 LEU
Chi-restraints excluded: chain G residue  514 SER
Chi-restraints excluded: chain G residue  549 THR
Chi-restraints excluded: chain G residue  551 VAL
Chi-restraints excluded: chain G residue  588 THR
Chi-restraints excluded: chain F residue    7 SER
Chi-restraints excluded: chain F residue   31 SER
Chi-restraints excluded: chain F residue  114 SER
Chi-restraints excluded: chain E residue   23 THR
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   62 ARG
Chi-restraints excluded: chain E residue   89 CYS
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  107 MET
Chi-restraints excluded: chain C residue  118 LEU
Chi-restraints excluded: chain D residue   75 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 80 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 50 optimal weight:    0.1980
   chunk 11 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 48 optimal weight:    0.0060
   chunk 60 optimal weight:    0.7980
   chunk 89 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
G 334 ASN
G 354 ASN
G 422 ASN
G 437 ASN
G 448 ASN
F  35 ASN
E  39 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.133288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.114737 restraints weight = 9884.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 2.01
r_work: 0.3394 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3252 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6995  Z= 0.126
  Angle     :  0.551   7.187   9586  Z= 0.290
  Chirality :  0.044   0.168   1055
  Planarity :  0.004   0.044   1260
  Dihedral  :  4.824  27.727   1037
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 18.56 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.60 (0.27), residues: 939
  helix: -3.94 (0.49), residues: 31
  sheet: -0.35 (0.27), residues: 354
  loop : -1.39 (0.26), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG F 100 
 TYR   0.017   0.001   TYR D  49 
 PHE   0.025   0.001   PHE B  29 
 TRP   0.012   0.002   TRP B  47 
 HIS   0.004   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6985)
  covalent geometry    : angle       0.55073 ( 9566)
  SS BOND              : bond        0.00346 (   10)
  SS BOND              : angle       0.61812 (   20)
  hydrogen bonds       : bond        0.03042 (  234)
  hydrogen bonds       : angle       5.88577 (  633)

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

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

  1878 Ramachandran restraints generated.
    939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1878 Ramachandran restraints generated.
    939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.192 
Fit side-chains
REVERT: A   63 PHE cc_start: 0.7815 (m-80) cc_final: 0.7496 (m-80)
REVERT: G  343 ASN cc_start: 0.8277 (t0) cc_final: 0.8010 (t0)
REVERT: G  439 ASN cc_start: 0.8407 (t0) cc_final: 0.7878 (t160)
REVERT: G  442 ASP cc_start: 0.7969 (m-30) cc_final: 0.7672 (m-30)
REVERT: G  443 SER cc_start: 0.8013 (p) cc_final: 0.7545 (p)
REVERT: F   34 MET cc_start: 0.8211 (mmm) cc_final: 0.7819 (mmt)
REVERT: D    4 MET cc_start: 0.7778 (mmm) cc_final: 0.7309 (mtp)
  outliers start: 17
  outliers final: 11
  residues processed: 123
  average time/residue: 0.2150
  time to fit residues: 29.8921
Evaluate side-chains
  123 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  452 LEU
Chi-restraints excluded: chain G residue  549 THR
Chi-restraints excluded: chain G residue  588 THR
Chi-restraints excluded: chain F residue  114 SER
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   62 ARG
Chi-restraints excluded: chain E residue   89 CYS
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain D residue   75 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0030
   chunk 19 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.6590

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

Flipped N/Q/H residues before XYZ refinement:
G 334 ASN
G 354 ASN
G 422 ASN
G 437 ASN
G 544 ASN
E  39 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.132687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.114166 restraints weight = 9734.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 1.99
r_work: 0.3383 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.2971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6995  Z= 0.167
  Angle     :  0.574   8.247   9586  Z= 0.302
  Chirality :  0.045   0.163   1055
  Planarity :  0.004   0.042   1260
  Dihedral  :  4.860  26.418   1037
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 17.90 %
    Favored  : 78.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.49 (0.27), residues: 939
  helix: -3.99 (0.47), residues: 31
  sheet: -0.21 (0.27), residues: 357
  loop : -1.36 (0.27), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F 100 
 TYR   0.019   0.002   TYR D  49 
 PHE   0.014   0.001   PHE B  93 
 TRP   0.013   0.002   TRP E  36 
 HIS   0.004   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 6985)
  covalent geometry    : angle       0.57401 ( 9566)
  SS BOND              : bond        0.00435 (   10)
  SS BOND              : angle       0.75165 (   20)
  hydrogen bonds       : bond        0.03237 (  234)
  hydrogen bonds       : angle       5.89662 (  633)

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

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

  1878 Ramachandran restraints generated.
    939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1878 Ramachandran restraints generated.
    939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.259 
Fit side-chains
REVERT: G  343 ASN cc_start: 0.8260 (t0) cc_final: 0.7994 (t0)
REVERT: G  439 ASN cc_start: 0.8427 (t0) cc_final: 0.7905 (t160)
REVERT: G  442 ASP cc_start: 0.7970 (m-30) cc_final: 0.7677 (m-30)
REVERT: G  443 SER cc_start: 0.7991 (p) cc_final: 0.7508 (p)
REVERT: F   34 MET cc_start: 0.8193 (mmm) cc_final: 0.7984 (mmt)
REVERT: D    4 MET cc_start: 0.7792 (mmm) cc_final: 0.7315 (mtp)
  outliers start: 22
  outliers final: 18
  residues processed: 123
  average time/residue: 0.1917
  time to fit residues: 26.6989
Evaluate side-chains
  129 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  415 THR
Chi-restraints excluded: chain G residue  452 LEU
Chi-restraints excluded: chain G residue  468 ILE
Chi-restraints excluded: chain G residue  494 SER
Chi-restraints excluded: chain G residue  514 SER
Chi-restraints excluded: chain G residue  549 THR
Chi-restraints excluded: chain G residue  551 VAL
Chi-restraints excluded: chain G residue  588 THR
Chi-restraints excluded: chain F residue    7 SER
Chi-restraints excluded: chain F residue  114 SER
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   62 ARG
Chi-restraints excluded: chain E residue   89 CYS
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain D residue   75 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 71 optimal weight:    0.0970
   chunk 6 optimal weight:    5.9990
   chunk 47 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
G 334 ASN
G 354 ASN
G 422 ASN
G 437 ASN
G 544 ASN
E  39 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.132863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.114368 restraints weight = 9811.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 2.00
r_work: 0.3386 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3244 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.3064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6995  Z= 0.166
  Angle     :  0.571   8.143   9586  Z= 0.301
  Chirality :  0.044   0.164   1055
  Planarity :  0.004   0.042   1260
  Dihedral  :  4.842  25.116   1037
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 18.88 %
    Favored  : 77.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.27), residues: 939
  helix: -3.97 (0.47), residues: 31
  sheet: -0.15 (0.27), residues: 357
  loop : -1.35 (0.27), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F 100 
 TYR   0.018   0.002   TYR D  49 
 PHE   0.013   0.001   PHE B  93 
 TRP   0.012   0.002   TRP E  36 
 HIS   0.004   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 6985)
  covalent geometry    : angle       0.57059 ( 9566)
  SS BOND              : bond        0.00429 (   10)
  SS BOND              : angle       0.75820 (   20)
  hydrogen bonds       : bond        0.03231 (  234)
  hydrogen bonds       : angle       5.85991 (  633)

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

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

  1878 Ramachandran restraints generated.
    939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1878 Ramachandran restraints generated.
    939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 0.251 
Fit side-chains
REVERT: G  343 ASN cc_start: 0.8251 (t0) cc_final: 0.7991 (t0)
REVERT: G  439 ASN cc_start: 0.8430 (t0) cc_final: 0.7893 (t160)
REVERT: G  442 ASP cc_start: 0.7966 (m-30) cc_final: 0.7673 (m-30)
REVERT: G  443 SER cc_start: 0.7996 (p) cc_final: 0.7525 (p)
REVERT: G  457 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7246 (ttm170)
REVERT: F   34 MET cc_start: 0.8187 (mmm) cc_final: 0.7803 (mmt)
REVERT: D    4 MET cc_start: 0.7798 (mmm) cc_final: 0.7319 (mtp)
  outliers start: 21
  outliers final: 17
  residues processed: 120
  average time/residue: 0.2117
  time to fit residues: 28.6900
Evaluate side-chains
  129 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  415 THR
Chi-restraints excluded: chain G residue  452 LEU
Chi-restraints excluded: chain G residue  457 ARG
Chi-restraints excluded: chain G residue  468 ILE
Chi-restraints excluded: chain G residue  549 THR
Chi-restraints excluded: chain G residue  551 VAL
Chi-restraints excluded: chain G residue  588 THR
Chi-restraints excluded: chain F residue    7 SER
Chi-restraints excluded: chain F residue  114 SER
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   62 ARG
Chi-restraints excluded: chain E residue   89 CYS
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain D residue   75 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 18 optimal weight:    0.1980
   chunk 83 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
G 354 ASN
G 422 ASN
G 437 ASN
G 544 ASN
E  39 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.132373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.113894 restraints weight = 9775.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 2.00
r_work: 0.3379 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.3114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6995  Z= 0.190
  Angle     :  0.588   8.140   9586  Z= 0.310
  Chirality :  0.045   0.162   1055
  Planarity :  0.004   0.042   1260
  Dihedral  :  4.925  24.772   1037
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 18.06 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.27), residues: 939
  helix: -3.99 (0.45), residues: 31
  sheet: -0.12 (0.27), residues: 357
  loop : -1.38 (0.26), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F 100 
 TYR   0.022   0.002   TYR G 508 
 PHE   0.033   0.002   PHE G 456 
 TRP   0.014   0.002   TRP E  36 
 HIS   0.004   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 6985)
  covalent geometry    : angle       0.58746 ( 9566)
  SS BOND              : bond        0.00473 (   10)
  SS BOND              : angle       0.82769 (   20)
  hydrogen bonds       : bond        0.03313 (  234)
  hydrogen bonds       : angle       5.91802 (  633)

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

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

  1878 Ramachandran restraints generated.
    939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1878 Ramachandran restraints generated.
    939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 114
  time to evaluate  : 0.172 
Fit side-chains
REVERT: G  343 ASN cc_start: 0.8272 (t0) cc_final: 0.7831 (t0)
REVERT: G  439 ASN cc_start: 0.8443 (t0) cc_final: 0.7914 (t160)
REVERT: G  442 ASP cc_start: 0.7970 (m-30) cc_final: 0.7672 (m-30)
REVERT: G  443 SER cc_start: 0.8001 (p) cc_final: 0.7507 (p)
REVERT: D    4 MET cc_start: 0.7792 (mmm) cc_final: 0.7317 (mtp)
  outliers start: 25
  outliers final: 19
  residues processed: 123
  average time/residue: 0.2067
  time to fit residues: 28.4335
Evaluate side-chains
  131 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  452 LEU
Chi-restraints excluded: chain G residue  468 ILE
Chi-restraints excluded: chain G residue  494 SER
Chi-restraints excluded: chain G residue  514 SER
Chi-restraints excluded: chain G residue  549 THR
Chi-restraints excluded: chain G residue  551 VAL
Chi-restraints excluded: chain G residue  588 THR
Chi-restraints excluded: chain F residue    7 SER
Chi-restraints excluded: chain F residue  114 SER
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   62 ARG
Chi-restraints excluded: chain E residue   89 CYS
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain D residue   75 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 34 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 73 optimal weight:    0.0870
   chunk 52 optimal weight:    0.4980
   chunk 75 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
G 334 ASN
G 354 ASN
G 422 ASN
G 437 ASN
G 544 ASN
E  39 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.133418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.115089 restraints weight = 9793.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 1.99
r_work: 0.3418 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3276 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6995  Z= 0.140
  Angle     :  0.562   8.346   9586  Z= 0.294
  Chirality :  0.044   0.165   1055
  Planarity :  0.004   0.043   1260
  Dihedral  :  4.725  22.954   1037
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 19.38 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.39 (0.27), residues: 939
  helix: -3.91 (0.49), residues: 31
  sheet: -0.08 (0.27), residues: 352
  loop : -1.33 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG G 403 
 TYR   0.023   0.002   TYR G 508 
 PHE   0.024   0.001   PHE G 456 
 TRP   0.012   0.002   TRP B  47 
 HIS   0.004   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 6985)
  covalent geometry    : angle       0.56136 ( 9566)
  SS BOND              : bond        0.00368 (   10)
  SS BOND              : angle       0.69159 (   20)
  hydrogen bonds       : bond        0.03057 (  234)
  hydrogen bonds       : angle       5.75605 (  633)

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

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

  1878 Ramachandran restraints generated.
    939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1878 Ramachandran restraints generated.
    939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.235 
Fit side-chains
REVERT: G  343 ASN cc_start: 0.8289 (t0) cc_final: 0.7852 (t0)
REVERT: G  439 ASN cc_start: 0.8443 (t0) cc_final: 0.7912 (t160)
REVERT: G  442 ASP cc_start: 0.7949 (m-30) cc_final: 0.7656 (m-30)
REVERT: G  443 SER cc_start: 0.8010 (p) cc_final: 0.7530 (p)
REVERT: D    4 MET cc_start: 0.7808 (mmm) cc_final: 0.7351 (mtp)
  outliers start: 19
  outliers final: 16
  residues processed: 117
  average time/residue: 0.1834
  time to fit residues: 24.3139
Evaluate side-chains
  126 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  415 THR
Chi-restraints excluded: chain G residue  468 ILE
Chi-restraints excluded: chain G residue  549 THR
Chi-restraints excluded: chain G residue  551 VAL
Chi-restraints excluded: chain G residue  588 THR
Chi-restraints excluded: chain F residue    7 SER
Chi-restraints excluded: chain F residue  114 SER
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   62 ARG
Chi-restraints excluded: chain E residue   89 CYS
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain D residue   75 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 26 optimal weight:    0.3980
   chunk 51 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 82 optimal weight:    2.9990
   chunk 28 optimal weight:    0.3980
   chunk 75 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
G 354 ASN
G 422 ASN
G 437 ASN
G 544 ASN
E  39 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.132970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.114358 restraints weight = 9732.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.03
r_work: 0.3405 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3263 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.3241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6995  Z= 0.171
  Angle     :  0.575   8.561   9586  Z= 0.301
  Chirality :  0.044   0.164   1055
  Planarity :  0.005   0.070   1260
  Dihedral  :  4.797  22.153   1037
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 19.54 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.36 (0.27), residues: 939
  helix: -3.98 (0.46), residues: 31
  sheet: -0.03 (0.27), residues: 358
  loop : -1.34 (0.26), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG G 403 
 TYR   0.023   0.002   TYR G 508 
 PHE   0.024   0.001   PHE G 456 
 TRP   0.013   0.002   TRP E  36 
 HIS   0.004   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 6985)
  covalent geometry    : angle       0.57496 ( 9566)
  SS BOND              : bond        0.00426 (   10)
  SS BOND              : angle       0.76679 (   20)
  hydrogen bonds       : bond        0.03203 (  234)
  hydrogen bonds       : angle       5.82604 (  633)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2089.62 seconds
wall clock time: 36 minutes 17.51 seconds (2177.51 seconds total)