Starting phenix.real_space_refine
on Wed Sep 17 08:36:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ja3_36124/09_2025/8ja3_36124.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ja3_36124/09_2025/8ja3_36124.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ja3_36124/09_2025/8ja3_36124.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ja3_36124/09_2025/8ja3_36124.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ja3_36124/09_2025/8ja3_36124.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ja3_36124/09_2025/8ja3_36124.map"
  }
  resolution = 3.94
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
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: 5
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     S      23      5.16       5
     C    4537      2.51       5
     N    1222      2.21       5
     O    1340      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7130
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "B"
      Number of atoms: 2118
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2118
          Classifications: {'peptide': 316}
          Incomplete info: {'truncation_to_alanine': 108}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 291}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 409
          Unresolved non-hydrogen angles: 501
          Unresolved non-hydrogen dihedrals: 338
          Unresolved non-hydrogen chiralities: 24
          Planarities with less than four sites: {'ASP:plan': 12, 'HIS:plan': 5, 'GLU:plan': 17, 'TYR:plan': 3, 'ARG:plan': 9, 'GLN:plan1': 5, 'ASN:plan1': 4, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 233
    Chain: "U"
      Number of atoms: 81
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 81
          Classifications: {'peptide': 10}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'TRANS': 9}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLU:plan': 2, 'TPO:plan-1': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "I"
      Number of atoms: 756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 756
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 2, 'TRANS': 104}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 110
          Unresolved non-hydrogen dihedrals: 73
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 3, 'GLU:plan': 2, 'TYR:plan': 3, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 66
    Chain: "M"
      Number of atoms: 680
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 680
          Classifications: {'peptide': 102}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 95}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 103
          Unresolved non-hydrogen angles: 125
          Unresolved non-hydrogen dihedrals: 83
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 4, 'ARG:plan': 2, 'GLU:plan': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 52
    Chain: "A"
      Number of atoms: 2070
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 309, 2070
          Classifications: {'peptide': 309}
          Incomplete info: {'truncation_to_alanine': 105}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 285}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 403
          Unresolved non-hydrogen angles: 494
          Unresolved non-hydrogen dihedrals: 335
          Unresolved non-hydrogen chiralities: 26
          Planarities with less than four sites: {'ARG:plan': 10, 'ASP:plan': 8, 'HIS:plan': 4, 'GLU:plan': 16, 'GLN:plan1': 3, 'ASN:plan1': 5, 'TYR:plan': 3, 'PHE:plan': 3}
          Unresolved non-hydrogen planarities: 224
    Chain: "V"
      Number of atoms: 81
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 81
          Classifications: {'peptide': 10}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'TRANS': 9}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLU:plan': 2, 'TPO:plan-1': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "H"
      Number of atoms: 684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 684
          Classifications: {'peptide': 99}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 2, 'TRANS': 96}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 97
          Unresolved non-hydrogen angles: 122
          Unresolved non-hydrogen dihedrals: 84
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'TYR:plan': 4, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 60
    Chain: "L"
      Number of atoms: 660
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 660
          Classifications: {'peptide': 100}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 94}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 109
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 92
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 4, 'ARG:plan': 2, 'PHE:plan': 1, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 55
  Time building chain proxies: 1.92, per 1000 atoms: 0.27
  Number of scatterers: 7130
  At special positions: 0
  Unit cell: (87.0348, 168.362, 79.9008, 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)
     S      23     16.00
     P       8     15.00
     O    1340      8.00
     N    1222      7.00
     C    4537      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS I  25 " - pdb=" SG  CYS I  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  24 " - pdb=" SG  CYS M  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " 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: 0.59
  Conformation dependent library (CDL) restraints added in 416.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1994

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 20 sheets defined
      6.4% alpha, 32.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'B' and resid 90 through 94
      removed outlier: 3.551A  pdb=" N   LYS B  94 " --> pdb=" O   PRO B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 109
      removed outlier: 3.587A  pdb=" N   LYS B 107 " --> pdb=" O   ARG B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 161
      No H-bonds generated for 'chain 'B' and resid 159 through 161'
    Processing helix  chain 'B' and resid 277 through 282
      removed outlier: 3.880A  pdb=" N   ASN B 280 " --> pdb=" O   PHE B 277 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 65 through 68
    Processing helix  chain 'I' and resid 77 through 79
      No H-bonds generated for 'chain 'I' and resid 77 through 79'
    Processing helix  chain 'I' and resid 90 through 94
      removed outlier: 3.866A  pdb=" N   THR I  94 " --> pdb=" O   ALA I  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 109
      removed outlier: 3.561A  pdb=" N   ARG A 103 " --> pdb=" O   ARG A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 282
      removed outlier: 3.506A  pdb=" N   ARG A 282 " --> pdb=" O   ALA A 279 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 31 through 35
    Processing helix  chain 'H' and resid 65 through 68
      removed outlier: 3.503A  pdb=" N   LYS H  68 " --> pdb=" O   ASP H  65 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 65 through 68'
    Processing helix  chain 'H' and resid 77 through 79
      No H-bonds generated for 'chain 'H' and resid 77 through 79'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 9 through 12
      removed outlier: 3.522A  pdb=" N   VAL B  41 " --> pdb=" O   TYR B 113 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   TYR B 113 " --> pdb=" O   VAL B  41 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 28
      removed outlier: 3.890A  pdb=" N   TYR B 144 " --> pdb=" O   ILE B 168 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   THR B  58 " --> pdb=" O   GLU B 145 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   PHE B  80 " --> pdb=" O   CYS B  59 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 127 through 129
    Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 187
      removed outlier: 3.818A  pdb=" N   SER B 202 " --> pdb=" O   ASN B 217 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   VAL B 218 " --> pdb=" O   LYS B 270 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   LYS B 270 " --> pdb=" O   VAL B 218 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 207 through 208
      removed outlier: 7.472A  pdb=" N   LEU B 351 " --> pdb=" O   VAL B 319 " (cutoff:3.500A)
      removed outlier: 9.495A  pdb=" N   VAL B 319 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   GLY B 316 " --> pdb=" O   CYS B 242 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ALA B 254 " --> pdb=" O   VAL B 235 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   GLN B 237 " --> pdb=" O   PRO B 252 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   ALA B 239 " --> pdb=" O   LYS B 250 " (cutoff:3.500A)
      removed outlier: 5.965A  pdb=" N   LYS B 250 " --> pdb=" O   ALA B 239 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   ILE B 241 " --> pdb=" O   GLN B 248 " (cutoff:3.500A)
      removed outlier: 5.228A  pdb=" N   GLN B 248 " --> pdb=" O   ILE B 241 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'I' and resid 7 through 10
      removed outlier: 3.931A  pdb=" N   LEU I  23 " --> pdb=" O   LEU I  84 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'I' and resid 61 through 63
      removed outlier: 6.070A  pdb=" N   TRP I  50 " --> pdb=" O   ARG I  41 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   ARG I  41 " --> pdb=" O   TRP I  50 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ALA I  52 " --> pdb=" O   TRP I  39 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'M' and resid 5 through 8
      removed outlier: 4.054A  pdb=" N   SER M   8 " --> pdb=" O   THR M  23 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   THR M  23 " --> pdb=" O   SER M   8 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'M' and resid 11 through 12
      removed outlier: 3.557A  pdb=" N   LEU M  12 " --> pdb=" O   LYS M 104 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'M' and resid 54 through 55
      removed outlier: 6.704A  pdb=" N   TRP M  36 " --> pdb=" O   LEU M  48 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   TYR M  50 " --> pdb=" O   VAL M  34 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   VAL M  34 " --> pdb=" O   TYR M  50 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   GLN M  91 " --> pdb=" O   THR M  98 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   THR M  98 " --> pdb=" O   GLN M  91 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 113 through 117
      removed outlier: 4.099A  pdb=" N   TYR A 113 " --> pdb=" O   VAL A  41 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   VAL A  41 " --> pdb=" O   TYR A 113 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 26 through 28
      removed outlier: 5.962A  pdb=" N   PHE A  27 " --> pdb=" O   VAL A 171 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   TYR A 144 " --> pdb=" O   ILE A 168 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   PHE A  80 " --> pdb=" O   CYS A  59 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 127 through 129
    Processing sheet with id=AB5, first strand: chain 'A' and resid 184 through 186
      removed outlier: 3.964A  pdb=" N   GLU A 200 " --> pdb=" O   HIS A 219 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   VAL A 218 " --> pdb=" O   LYS A 270 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   LYS A 270 " --> pdb=" O   VAL A 218 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 207 through 208
      removed outlier: 3.785A  pdb=" N   TYR A 321 " --> pdb=" O   PHE A 349 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   LEU A 351 " --> pdb=" O   VAL A 319 " (cutoff:3.500A)
      removed outlier: 8.433A  pdb=" N   VAL A 319 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   LYS A 322 " --> pdb=" O   ARG A 236 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ARG A 236 " --> pdb=" O   LYS A 322 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   ILE A 231 " --> pdb=" O   GLU A 257 " (cutoff:3.500A)
      removed outlier: 5.584A  pdb=" N   GLU A 257 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 7.488A  pdb=" N   ILE A 233 " --> pdb=" O   MET A 255 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   MET A 255 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   VAL A 235 " --> pdb=" O   VAL A 253 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AB8, first strand: chain 'H' and resid 61 through 63
      removed outlier: 5.722A  pdb=" N   TRP H  50 " --> pdb=" O   ARG H  41 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   ARG H  41 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ALA H  52 " --> pdb=" O   TRP H  39 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   TYR H 112 " --> pdb=" O   ARG H 101 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'L' and resid 6 through 8
      removed outlier: 3.569A  pdb=" N   PHE L  72 " --> pdb=" O   CYS L  24 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'L' and resid 11 through 12
      removed outlier: 3.779A  pdb=" N   LEU L  12 " --> pdb=" O   LYS L 104 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC1
    Processing sheet with id=AC2, first strand: chain 'L' and resid 54 through 55
      removed outlier: 6.424A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)

    254 hydrogen bonds defined for protein.
    627 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: 0.95

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2126
        1.33 -     1.46: 1243
        1.46 -     1.58: 3860
        1.58 -     1.70: 17
        1.70 -     1.82: 28
  Bond restraints: 7274
  Sorted by residual:
  bond pdb=" C   LEU A  33 "
       pdb=" N   VAL A  34 "
    ideal  model  delta    sigma   weight residual
    1.330  1.470 -0.140 1.97e-02 2.58e+03 5.04e+01
  bond pdb=" OG1 TPO V 463 "
       pdb=" P   TPO V 463 "
    ideal  model  delta    sigma   weight residual
    1.717  1.598  0.119 2.00e-02 2.50e+03 3.52e+01
  bond pdb=" OG1 TPO V 466 "
       pdb=" P   TPO V 466 "
    ideal  model  delta    sigma   weight residual
    1.717  1.602  0.115 2.00e-02 2.50e+03 3.31e+01
  bond pdb=" OG1 TPO U 463 "
       pdb=" P   TPO U 463 "
    ideal  model  delta    sigma   weight residual
    1.717  1.602  0.115 2.00e-02 2.50e+03 3.29e+01
  bond pdb=" OG1 TPO U 466 "
       pdb=" P   TPO U 466 "
    ideal  model  delta    sigma   weight residual
    1.717  1.607  0.110 2.00e-02 2.50e+03 3.01e+01
  ... (remaining 7269 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.20: 9854
        3.20 -     6.40: 144
        6.40 -     9.60: 5
        9.60 -    12.80: 3
       12.80 -    16.00: 2
  Bond angle restraints: 10008
  Sorted by residual:
  angle pdb=" C   LEU A  33 "
        pdb=" N   VAL A  34 "
        pdb=" CA  VAL A  34 "
      ideal   model   delta    sigma   weight residual
     122.91  133.35  -10.44 1.43e+00 4.89e-01 5.33e+01
  angle pdb=" N   SEP U 465 "
        pdb=" CA  SEP U 465 "
        pdb=" C   SEP U 465 "
      ideal   model   delta    sigma   weight residual
     111.20  127.20  -16.00 2.80e+00 1.28e-01 3.27e+01
  angle pdb=" O   LEU A  33 "
        pdb=" C   LEU A  33 "
        pdb=" N   VAL A  34 "
      ideal   model   delta    sigma   weight residual
     123.17  117.27    5.90 1.21e+00 6.83e-01 2.37e+01
  angle pdb=" N   ARG U 464 "
        pdb=" CA  ARG U 464 "
        pdb=" C   ARG U 464 "
      ideal   model   delta    sigma   weight residual
     111.00  124.31  -13.31 2.80e+00 1.28e-01 2.26e+01
  angle pdb=" C   SER L  31 "
        pdb=" CA  SER L  31 "
        pdb=" CB  SER L  31 "
      ideal   model   delta    sigma   weight residual
     116.54  111.36    5.18 1.15e+00 7.56e-01 2.03e+01
  ... (remaining 10003 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.26: 3891
       17.26 -    34.53: 300
       34.53 -    51.79: 53
       51.79 -    69.05: 14
       69.05 -    86.31: 4
  Dihedral angle restraints: 4262
    sinusoidal: 1196
      harmonic: 3066
  Sorted by residual:
  dihedral pdb=" CB  CYS H  25 "
           pdb=" SG  CYS H  25 "
           pdb=" SG  CYS H  99 "
           pdb=" CB  CYS H  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   39.38   53.62     1      1.00e+01 1.00e-02 3.91e+01
  dihedral pdb=" CA  ARG B 169 "
           pdb=" C   ARG B 169 "
           pdb=" N   LYS B 170 "
           pdb=" CA  LYS B 170 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.80   26.20     0      5.00e+00 4.00e-02 2.75e+01
  dihedral pdb=" CA  LEU I 110 "
           pdb=" C   LEU I 110 "
           pdb=" N   ASP I 111 "
           pdb=" CA  ASP I 111 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.39  -24.61     0      5.00e+00 4.00e-02 2.42e+01
  ... (remaining 4259 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1036
       0.069 -    0.137: 166
       0.137 -    0.206: 11
       0.206 -    0.275: 3
       0.275 -    0.344: 1
  Chirality restraints: 1217
  Sorted by residual:
  chirality pdb=" CA  SEP U 465 "
            pdb=" N   SEP U 465 "
            pdb=" C   SEP U 465 "
            pdb=" CB  SEP U 465 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50    2.16    0.34 2.00e-01 2.50e+01 2.95e+00
  chirality pdb=" CA  ARG U 464 "
            pdb=" N   ARG U 464 "
            pdb=" C   ARG U 464 "
            pdb=" CB  ARG U 464 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CB  TPO U 463 "
            pdb=" CA  TPO U 463 "
            pdb=" OG1 TPO U 463 "
            pdb=" CG2 TPO U 463 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.72   -0.24 2.00e-01 2.50e+01 1.45e+00
  ... (remaining 1214 not shown)

  Planarity restraints: 1284
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER I 102 "   -0.024 2.00e-02 2.50e+03   4.73e-02 2.23e+01
        pdb=" C   SER I 102 "    0.082 2.00e-02 2.50e+03
        pdb=" O   SER I 102 "   -0.030 2.00e-02 2.50e+03
        pdb=" N   ARG I 103 "   -0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU U 462 "   -0.023 2.00e-02 2.50e+03   4.68e-02 2.19e+01
        pdb=" C   LEU U 462 "    0.081 2.00e-02 2.50e+03
        pdb=" O   LEU U 462 "   -0.031 2.00e-02 2.50e+03
        pdb=" N   TPO U 463 "   -0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SEP U 459 "    0.019 2.00e-02 2.50e+03   3.68e-02 1.36e+01
        pdb=" C   SEP U 459 "   -0.064 2.00e-02 2.50e+03
        pdb=" O   SEP U 459 "    0.024 2.00e-02 2.50e+03
        pdb=" N   GLU U 460 "    0.021 2.00e-02 2.50e+03
  ... (remaining 1281 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1427
        2.77 -     3.30: 6975
        3.30 -     3.84: 11066
        3.84 -     4.37: 12499
        4.37 -     4.90: 21638
  Nonbonded interactions: 53605
  Sorted by model distance:
  nonbonded pdb=" N   GLY L  17 "
            pdb=" O   LEU L  79 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" O   ASN H  80 "
            pdb=" OD1 ASN H  80 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OE1 GLN B 172 "
            pdb=" OG1 THR B 304 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   PHE H  30 "
            pdb=" ND2 ASN H  80 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" O   THR A 221 "
            pdb=" OG1 THR A 221 "
     model   vdw
     2.289 3.040
  ... (remaining 53600 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 7 through 45 or (resid 46 through 51 and (name N or name C \ 
A or name C or name O or name CB )) or resid 52 through 100 or (resid 101 throug \ 
h 102 and (name N or name CA or name C or name O or name CB )) or resid 103 thro \ 
ugh 122 or (resid 123 and (name N or name CA or name C or name O or name CB )) o \ 
r resid 124 through 184 or (resid 185 and (name N or name CA or name C or name O \ 
 or name CB )) or resid 186 through 193 or (resid 194 through 195 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 196 through 209 or (resid 21 \ 
0 and (name N or name CA or name C or name O or name CB )) or resid 211 or (resi \ 
d 212 and (name N or name CA or name C or name O or name CB )) or resid 213 thro \ 
ugh 220 or (resid 221 through 222 and (name N or name CA or name C or name O or  \ 
name CB )) or resid 223 through 227 or (resid 228 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 229 through 239 or (resid 240 through 241 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 242 through 247  \ 
or (resid 248 through 251 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 252 through 255 or (resid 256 through 261 and (name N or name CA or  \ 
name C or name O or name CB )) or resid 262 through 266 or (resid 267 and (name  \ 
N or name CA or name C or name O or name CB )) or resid 268 through 288 or (resi \ 
d 289 through 290 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 291 through 299 or (resid 300 through 301 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 302 through 325 or (resid 326 through 327 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 328 through 357))
  selection = (chain 'B' and ((resid 7 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 8 through 41 or resid 45 through 47 or (resid 48 through 51 and (name \ 
 N or name CA or name C or name O or name CB )) or resid 52 through 61 or resid  \ 
77 through 89 or (resid 92 through 95 and (name N or name CA or name C or name O \ 
 or name CB )) or resid 96 through 121 or (resid 122 through 123 and (name N or  \ 
name CA or name C or name O or name CB )) or resid 124 through 131 or (resid 139 \ 
 through 145 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 
46 through 148 or (resid 149 through 157 and (name N or name CA or name C or nam \ 
e O or name CB )) or resid 158 through 160 or (resid 161 and (name N or name CA  \ 
or name C or name O or name CB )) or resid 162 through 189 or (resid 190 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 193 through 198 or (r \ 
esid 199 through 201 and (name N or name CA or name C or name O or name CB )) or \ 
 resid 202 through 205 or (resid 206 through 207 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 208 through 217 or (resid 218 through 219 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 220 through 226 o \ 
r (resid 227 through 228 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 229 through 240 or (resid 241 and (name N or name CA or name C or nam \ 
e O or name CB )) or resid 242 through 286 or (resid 287 through 290 and (name N \ 
 or name CA or name C or name O or name CB )) or resid 291 through 349 or (resid \ 
 350 and (name N or name CA or name C or name O or name CB )) or resid 351 throu \ 
gh 357))
}
ncs_group {
  reference = (chain 'H' and (resid 5 through 9 or (resid 10 and (name N or name CA or name C  \ 
or name O or name CB )) or resid 11 through 47 or (resid 48 through 49 and (name \ 
 N or name CA or name C or name O or name CB )) or resid 50 through 69 or (resid \ 
 70 and (name N or name CA or name C or name O or name CB )) or resid 71 through \ 
 103 or resid 106 through 111 or (resid 112 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 113 through 114 or (resid 115 and (name N or name  \ 
CA or name C or name O or name CB ))))
  selection = (chain 'I' and (resid 5 through 8 or (resid 9 through 10 and (name N or name CA  \ 
or name C or name O or name CB )) or resid 11 through 19 or (resid 20 and (name  \ 
N or name CA or name C or name O or name CB )) or resid 21 or (resid 22 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 23 through 27 or (resi \ 
d 28 and (name N or name CA or name C or name O or name CB )) or resid 29 throug \ 
h 33 or (resid 34 through 36 and (name N or name CA or name C or name O or name  \ 
CB )) or resid 37 through 55 or (resid 56 through 58 and (name N or name CA or n \ 
ame C or name O or name CB )) or (resid 59 through 61 and (name N or name CA or  \ 
name C or name O or name CB )) or resid 62 through 67 or (resid 68 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 69 through 72 or (resid 73  \ 
through 76 and (name N or name CA or name C or name O or name CB )) or resid 77  \ 
through 78 or (resid 79 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 80 through 82 or (resid 83 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 93 or (resid 94 through 95 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 96 through 115))
}
ncs_group {
  reference = (chain 'L' and (resid 2 through 5 or (resid 6 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 7 or (resid 8 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 9 through 10 or (resid 11 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 12 through 17 or (resid 18 through 2 \ 
3 and (name N or name CA or name C or name O or name CB )) or resid 24 through 2 \ 
6 or (resid 27 through 29 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 30 through 39 or (resid 40 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 41 through 73 or (resid 74 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 75 through 79 or (resid 82 through 87 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 88 through 105 or  \ 
(resid 106 and (name N or name CA or name C or name O or name CB ))))
  selection = (chain 'M' and (resid 2 through 21 or (resid 22 through 23 and (name N or name C \ 
A or name C or name O or name CB )) or resid 24 through 28 or (resid 29 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 30 or (resid 31 throug \ 
h 33 and (name N or name CA or name C or name O or name CB )) or resid 34 throug \ 
h 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name  \ 
CB )) or resid 41 through 45 or (resid 46 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 47 through 67 or (resid 68 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 69 through 79 or (resid 82 through 87 a \ 
nd (name N or name CA or name C or name O or name CB )) or resid 88 through 93 o \ 
r (resid 94 and (name N or name CA or name C or name O or name CB )) or resid 95 \ 
 through 104 or (resid 105 through 106 and (name N or name CA or name C or name  \ 
O or name CB ))))
}
ncs_group {
  reference = chain 'U'
  selection = chain 'V'
}

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:             1.290
  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:             0.020
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.220
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5886
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      :  0.007   0.140   7278  Z= 0.360
  Angle     :  0.941  16.005  10016  Z= 0.508
  Chirality :  0.051   0.344   1217
  Planarity :  0.007   0.082   1284
  Dihedral  : 14.002  86.312   2256
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 17.01 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.46 (0.26), residues: 987
  helix: -1.26 (0.98), residues: 22
  sheet: -0.94 (0.26), residues: 391
  loop : -0.92 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 282 
 TYR   0.032   0.003   TYR B 321 
 PHE   0.018   0.002   PHE B 349 
 TRP   0.012   0.002   TRP H  50 
 HIS   0.011   0.002   HIS I  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00698 ( 7274)
  covalent geometry    : angle       0.94077 (10008)
  SS BOND              : bond        0.00315 (    4)
  SS BOND              : angle       1.31475 (    8)
  hydrogen bonds       : bond        0.25644 (  254)
  hydrogen bonds       : angle      10.67420 (  627)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 143
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  158 ILE cc_start: 0.7224 (mm) cc_final: 0.6869 (mt)
REVERT: I   78 SER cc_start: 0.7651 (m) cc_final: 0.7294 (p)
REVERT: I  103 ARG cc_start: 0.3686 (OUTLIER) cc_final: 0.3454 (ttp80)
REVERT: M   49 ILE cc_start: 0.7847 (mt) cc_final: 0.7322 (mp)
REVERT: M   90 GLN cc_start: 0.7017 (tm-30) cc_final: 0.6582 (tm-30)
REVERT: A  103 ARG cc_start: 0.3486 (OUTLIER) cc_final: 0.2304 (mtm-85)
REVERT: A  169 ARG cc_start: 0.6389 (mtp180) cc_final: 0.6076 (mtp-110)
REVERT: A  326 LYS cc_start: 0.5016 (OUTLIER) cc_final: 0.3323 (tptt)
REVERT: L   49 ILE cc_start: 0.7721 (mm) cc_final: 0.7361 (mm)
  outliers start: 13
  outliers final: 5
  residues processed: 150
  average time/residue: 0.1074
  time to fit residues: 20.5869
Evaluate side-chains
  130 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 122
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  281 ASN
Chi-restraints excluded: chain I residue  103 ARG
Chi-restraints excluded: chain A residue   11 LYS
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  103 ARG
Chi-restraints excluded: chain A residue  326 LYS
Chi-restraints excluded: chain H residue   31 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0770
   chunk 100 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0010
   overall best weight:    0.4144

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

Flipped N/Q/H residues before XYZ refinement:
A  83 ASN
A 237 GLN
L  38 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.180836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.164825 restraints weight = 13023.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.167276 restraints weight = 9523.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.169058 restraints weight = 7397.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.170396 restraints weight = 6051.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.171364 restraints weight = 5131.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.4338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5895
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7278  Z= 0.137
  Angle     :  0.682  11.347  10016  Z= 0.348
  Chirality :  0.046   0.209   1217
  Planarity :  0.005   0.050   1284
  Dihedral  :  7.742  75.671   1135
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 18.06 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.93 (0.27), residues: 987
  helix:  0.71 (1.12), residues: 22
  sheet: -0.66 (0.26), residues: 414
  loop : -0.54 (0.27), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  25 
 TYR   0.023   0.002   TYR H 112 
 PHE   0.018   0.002   PHE B 349 
 TRP   0.015   0.002   TRP I  39 
 HIS   0.004   0.001   HIS I  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 7274)
  covalent geometry    : angle       0.68116 (10008)
  SS BOND              : bond        0.00595 (    4)
  SS BOND              : angle       1.25467 (    8)
  hydrogen bonds       : bond        0.03389 (  254)
  hydrogen bonds       : angle       6.87204 (  627)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 141
  time to evaluate  : 0.236 
Fit side-chains
REVERT: B   61 PHE cc_start: 0.5151 (t80) cc_final: 0.4947 (t80)
REVERT: B  275 THR cc_start: 0.5208 (m) cc_final: 0.4991 (m)
REVERT: I   78 SER cc_start: 0.7688 (m) cc_final: 0.7325 (p)
REVERT: M   49 ILE cc_start: 0.7849 (mt) cc_final: 0.7395 (tt)
REVERT: M   90 GLN cc_start: 0.7233 (tm-30) cc_final: 0.6929 (tm-30)
REVERT: A  103 ARG cc_start: 0.4130 (OUTLIER) cc_final: 0.2866 (mtm-85)
REVERT: L   49 ILE cc_start: 0.7377 (mm) cc_final: 0.7094 (mm)
  outliers start: 25
  outliers final: 16
  residues processed: 151
  average time/residue: 0.0811
  time to fit residues: 16.3986
Evaluate side-chains
  151 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain I residue   54 ILE
Chi-restraints excluded: chain I residue   94 THR
Chi-restraints excluded: chain M residue   34 VAL
Chi-restraints excluded: chain M residue   78 SER
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain A residue   83 ASN
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  103 ARG
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 101 optimal weight:    3.9990
   chunk 76 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0670
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
B  83 ASN
I  38 HIS
A 237 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.179513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.163781 restraints weight = 12915.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.166217 restraints weight = 9389.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.167994 restraints weight = 7285.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.169064 restraints weight = 5945.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.170173 restraints weight = 5122.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.4321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5926
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7278  Z= 0.154
  Angle     :  0.653  11.336  10016  Z= 0.329
  Chirality :  0.046   0.214   1217
  Planarity :  0.005   0.052   1284
  Dihedral  :  6.832  74.508   1119
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 20.14 %
    Favored  : 75.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.90 (0.28), residues: 987
  helix:  1.32 (1.16), residues: 22
  sheet: -0.68 (0.26), residues: 414
  loop : -0.50 (0.27), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  25 
 TYR   0.018   0.002   TYR I  98 
 PHE   0.015   0.002   PHE B 349 
 TRP   0.028   0.002   TRP I  39 
 HIS   0.005   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 7274)
  covalent geometry    : angle       0.65274 (10008)
  SS BOND              : bond        0.00275 (    4)
  SS BOND              : angle       0.95036 (    8)
  hydrogen bonds       : bond        0.03150 (  254)
  hydrogen bonds       : angle       6.27412 (  627)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 134
  time to evaluate  : 0.304 
Fit side-chains
REVERT: B  275 THR cc_start: 0.5320 (m) cc_final: 0.5107 (m)
REVERT: I   78 SER cc_start: 0.7630 (m) cc_final: 0.7225 (p)
REVERT: M   49 ILE cc_start: 0.7794 (mt) cc_final: 0.7393 (tt)
REVERT: M   90 GLN cc_start: 0.7226 (tm-30) cc_final: 0.6924 (tm-30)
REVERT: H  110 LEU cc_start: 0.7342 (mp) cc_final: 0.7067 (mt)
REVERT: L   49 ILE cc_start: 0.7278 (mm) cc_final: 0.6968 (mm)
  outliers start: 26
  outliers final: 17
  residues processed: 146
  average time/residue: 0.0835
  time to fit residues: 16.2039
Evaluate side-chains
  150 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain I residue   54 ILE
Chi-restraints excluded: chain I residue   94 THR
Chi-restraints excluded: chain M residue   34 VAL
Chi-restraints excluded: chain M residue   89 CYS
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  229 LYS
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9990
   chunk 73 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 54 optimal weight:    0.2980
   chunk 51 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B  83 ASN
B 245 ASN
A 101 GLN
A 237 GLN
L  38 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.177790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.163824 restraints weight = 13102.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.165743 restraints weight = 10015.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.167109 restraints weight = 8059.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.168181 restraints weight = 6787.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.168971 restraints weight = 5894.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.4304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5956
moved from start:          0.2889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7278  Z= 0.177
  Angle     :  0.664  10.944  10016  Z= 0.336
  Chirality :  0.046   0.280   1217
  Planarity :  0.005   0.058   1284
  Dihedral  :  6.513  74.883   1115
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 20.14 %
    Favored  : 74.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.96 (0.28), residues: 987
  helix:  0.83 (1.12), residues: 24
  sheet: -0.69 (0.26), residues: 405
  loop : -0.57 (0.28), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  25 
 TYR   0.026   0.002   TYR H  98 
 PHE   0.015   0.002   PHE B 349 
 TRP   0.037   0.003   TRP I  39 
 HIS   0.003   0.001   HIS A 353 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 7274)
  covalent geometry    : angle       0.66324 (10008)
  SS BOND              : bond        0.00374 (    4)
  SS BOND              : angle       0.96838 (    8)
  hydrogen bonds       : bond        0.03100 (  254)
  hydrogen bonds       : angle       6.21236 (  627)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 134
  time to evaluate  : 0.267 
Fit side-chains
REVERT: B  295 HIS cc_start: 0.7312 (OUTLIER) cc_final: 0.6324 (t-90)
REVERT: I   55 SER cc_start: 0.6746 (t) cc_final: 0.6165 (p)
REVERT: I   78 SER cc_start: 0.7601 (m) cc_final: 0.7201 (p)
REVERT: M   49 ILE cc_start: 0.7836 (mt) cc_final: 0.7473 (tt)
REVERT: M   90 GLN cc_start: 0.7246 (tm-30) cc_final: 0.6934 (tm-30)
REVERT: A  320 SER cc_start: 0.7550 (t) cc_final: 0.6999 (p)
  outliers start: 32
  outliers final: 23
  residues processed: 152
  average time/residue: 0.0809
  time to fit residues: 16.7175
Evaluate side-chains
  156 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 ASP
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  295 HIS
Chi-restraints excluded: chain I residue   53 SER
Chi-restraints excluded: chain I residue   54 ILE
Chi-restraints excluded: chain I residue   94 THR
Chi-restraints excluded: chain M residue   34 VAL
Chi-restraints excluded: chain M residue   89 CYS
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain A residue   80 PHE
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  229 LYS
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   55 LEU
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   95 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0070
   chunk 35 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 4 optimal weight:    0.2980
   chunk 95 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0370
   chunk 59 optimal weight:    0.8980
   chunk 98 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    0.3876

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

Flipped N/Q/H residues before XYZ refinement:
A 237 GLN
L  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4470 r_free = 0.4470 target = 0.180688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.164875 restraints weight = 13131.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.167369 restraints weight = 9497.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.169126 restraints weight = 7327.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.170458 restraints weight = 5972.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.171266 restraints weight = 5056.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.4335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5903
moved from start:          0.3262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7278  Z= 0.123
  Angle     :  0.593   7.599  10016  Z= 0.299
  Chirality :  0.043   0.192   1217
  Planarity :  0.005   0.047   1284
  Dihedral  :  6.401  75.909   1115
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 23.78 %
    Favored  : 71.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.89 (0.28), residues: 987
  helix:  1.18 (1.16), residues: 24
  sheet: -0.61 (0.27), residues: 409
  loop : -0.56 (0.28), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 101 
 TYR   0.013   0.002   TYR B 321 
 PHE   0.016   0.001   PHE B 349 
 TRP   0.038   0.002   TRP I  39 
 HIS   0.002   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7274)
  covalent geometry    : angle       0.59292 (10008)
  SS BOND              : bond        0.00277 (    4)
  SS BOND              : angle       0.74803 (    8)
  hydrogen bonds       : bond        0.02572 (  254)
  hydrogen bonds       : angle       5.70792 (  627)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 137
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.5801 (mmm-85) cc_final: 0.5222 (mmm-85)
REVERT: B  113 TYR cc_start: 0.7226 (m-80) cc_final: 0.6507 (m-80)
REVERT: B  233 ILE cc_start: 0.0746 (OUTLIER) cc_final: 0.0437 (mt)
REVERT: B  295 HIS cc_start: 0.7112 (OUTLIER) cc_final: 0.6218 (t-90)
REVERT: I   55 SER cc_start: 0.6788 (t) cc_final: 0.6410 (p)
REVERT: I   78 SER cc_start: 0.7630 (m) cc_final: 0.7217 (p)
REVERT: M   49 ILE cc_start: 0.7764 (mt) cc_final: 0.7442 (tt)
REVERT: M   90 GLN cc_start: 0.7244 (tm-30) cc_final: 0.6940 (tm-30)
REVERT: A  278 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6274 (pp)
REVERT: A  320 SER cc_start: 0.7430 (t) cc_final: 0.6919 (p)
REVERT: H   50 TRP cc_start: 0.6985 (t60) cc_final: 0.6732 (t60)
REVERT: L   78 SER cc_start: 0.7266 (m) cc_final: 0.6938 (p)
  outliers start: 28
  outliers final: 20
  residues processed: 151
  average time/residue: 0.0847
  time to fit residues: 17.3476
Evaluate side-chains
  156 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 133
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  229 LYS
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  295 HIS
Chi-restraints excluded: chain I residue   54 ILE
Chi-restraints excluded: chain I residue   94 THR
Chi-restraints excluded: chain M residue   34 VAL
Chi-restraints excluded: chain M residue   89 CYS
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  229 LYS
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain L residue   34 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 47 optimal weight:    0.3980
   chunk 76 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 96 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 50 optimal weight:    0.5980
   chunk 57 optimal weight:    0.0570
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.4498

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

Flipped N/Q/H residues before XYZ refinement:
B  83 ASN
A 237 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.180086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.164262 restraints weight = 13115.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.166666 restraints weight = 9516.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.168162 restraints weight = 7401.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.169676 restraints weight = 6141.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.170517 restraints weight = 5190.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.4328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5926
moved from start:          0.3451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7278  Z= 0.133
  Angle     :  0.592   7.378  10016  Z= 0.297
  Chirality :  0.044   0.195   1217
  Planarity :  0.005   0.048   1284
  Dihedral  :  6.399  75.668   1115
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 25.17 %
    Favored  : 68.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.90 (0.28), residues: 987
  helix:  1.20 (1.16), residues: 24
  sheet: -0.59 (0.27), residues: 409
  loop : -0.60 (0.28), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 282 
 TYR   0.016   0.002   TYR H  98 
 PHE   0.015   0.001   PHE B 349 
 TRP   0.041   0.002   TRP I  39 
 HIS   0.003   0.001   HIS A 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7274)
  covalent geometry    : angle       0.59188 (10008)
  SS BOND              : bond        0.00294 (    4)
  SS BOND              : angle       0.73028 (    8)
  hydrogen bonds       : bond        0.02598 (  254)
  hydrogen bonds       : angle       5.62592 (  627)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 136
  time to evaluate  : 0.186 
Fit side-chains
REVERT: B  173 TYR cc_start: 0.6121 (m-80) cc_final: 0.5349 (m-10)
REVERT: B  233 ILE cc_start: 0.0368 (OUTLIER) cc_final: 0.0027 (mt)
REVERT: B  295 HIS cc_start: 0.7174 (OUTLIER) cc_final: 0.6249 (t-90)
REVERT: I   55 SER cc_start: 0.6657 (t) cc_final: 0.6073 (p)
REVERT: I   78 SER cc_start: 0.7615 (m) cc_final: 0.7214 (p)
REVERT: M   49 ILE cc_start: 0.7770 (mt) cc_final: 0.7427 (tt)
REVERT: M   90 GLN cc_start: 0.7247 (tm-30) cc_final: 0.6894 (tm-30)
REVERT: A  278 LEU cc_start: 0.6492 (OUTLIER) cc_final: 0.6238 (pp)
REVERT: A  320 SER cc_start: 0.7427 (t) cc_final: 0.6920 (p)
REVERT: A  346 GLU cc_start: 0.6219 (mp0) cc_final: 0.5928 (mp0)
REVERT: H   50 TRP cc_start: 0.6981 (t60) cc_final: 0.6585 (t60)
REVERT: L   38 GLN cc_start: 0.4566 (tt0) cc_final: 0.4184 (mm-40)
REVERT: L   49 ILE cc_start: 0.7181 (tp) cc_final: 0.6932 (tp)
REVERT: L   78 SER cc_start: 0.7272 (m) cc_final: 0.6966 (p)
  outliers start: 35
  outliers final: 26
  residues processed: 154
  average time/residue: 0.0775
  time to fit residues: 16.3460
Evaluate side-chains
  163 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 134
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 ASP
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  229 LYS
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  295 HIS
Chi-restraints excluded: chain I residue   37 ILE
Chi-restraints excluded: chain I residue   54 ILE
Chi-restraints excluded: chain I residue   94 THR
Chi-restraints excluded: chain M residue   34 VAL
Chi-restraints excluded: chain M residue   89 CYS
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain A residue   35 ASP
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  229 LYS
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   95 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 95 optimal weight:    0.3980
   chunk 66 optimal weight:    0.5980
   chunk 94 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 83 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 63 optimal weight:    6.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 237 GLN
L  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.177012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.163101 restraints weight = 12994.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.164963 restraints weight = 9960.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.166344 restraints weight = 8053.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.167388 restraints weight = 6801.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.168018 restraints weight = 5908.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.4296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5995
moved from start:          0.3613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7278  Z= 0.198
  Angle     :  0.672   6.933  10016  Z= 0.339
  Chirality :  0.046   0.207   1217
  Planarity :  0.005   0.057   1284
  Dihedral  :  6.682  74.362   1115
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  7.29 %
    Allowed  : 25.52 %
    Favored  : 67.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.07 (0.28), residues: 987
  helix:  0.88 (1.13), residues: 24
  sheet: -0.73 (0.26), residues: 411
  loop : -0.68 (0.28), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG M  67 
 TYR   0.022   0.002   TYR I  98 
 PHE   0.014   0.002   PHE B 349 
 TRP   0.053   0.003   TRP I  39 
 HIS   0.006   0.001   HIS A 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 7274)
  covalent geometry    : angle       0.67134 (10008)
  SS BOND              : bond        0.00369 (    4)
  SS BOND              : angle       0.86247 (    8)
  hydrogen bonds       : bond        0.03198 (  254)
  hydrogen bonds       : angle       6.23470 (  627)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 137
  time to evaluate  : 0.267 
Fit side-chains
REVERT: B  173 TYR cc_start: 0.6017 (m-80) cc_final: 0.5238 (m-10)
REVERT: B  233 ILE cc_start: 0.0747 (OUTLIER) cc_final: 0.0319 (mt)
REVERT: B  295 HIS cc_start: 0.7150 (OUTLIER) cc_final: 0.6066 (t-90)
REVERT: I   55 SER cc_start: 0.7052 (t) cc_final: 0.6528 (p)
REVERT: I   78 SER cc_start: 0.7644 (m) cc_final: 0.7238 (p)
REVERT: M   49 ILE cc_start: 0.7837 (mt) cc_final: 0.7517 (tt)
REVERT: M   62 ARG cc_start: 0.6390 (ptt90) cc_final: 0.6099 (ptt90)
REVERT: M   90 GLN cc_start: 0.7165 (tm-30) cc_final: 0.6861 (tm-30)
REVERT: A  278 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6404 (pp)
REVERT: A  320 SER cc_start: 0.7481 (t) cc_final: 0.6927 (p)
REVERT: L   38 GLN cc_start: 0.4822 (tt0) cc_final: 0.4047 (mm-40)
REVERT: L   49 ILE cc_start: 0.7296 (tp) cc_final: 0.7079 (tp)
  outliers start: 42
  outliers final: 26
  residues processed: 161
  average time/residue: 0.0838
  time to fit residues: 18.6753
Evaluate side-chains
  160 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 131
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  229 LYS
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  295 HIS
Chi-restraints excluded: chain I residue   51 VAL
Chi-restraints excluded: chain I residue   53 SER
Chi-restraints excluded: chain I residue   54 ILE
Chi-restraints excluded: chain I residue   94 THR
Chi-restraints excluded: chain M residue   34 VAL
Chi-restraints excluded: chain M residue   51 SER
Chi-restraints excluded: chain M residue   89 CYS
Chi-restraints excluded: chain M residue   95 VAL
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain A residue   35 ASP
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  229 LYS
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   95 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   chunk 22 optimal weight:    0.1980
   chunk 35 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   chunk 66 optimal weight:    0.0470
   chunk 68 optimal weight:    6.9990
   chunk 8 optimal weight:    0.7980
   chunk 17 optimal weight:    4.9990
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
A 237 GLN
L  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.178908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.165111 restraints weight = 13141.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.166998 restraints weight = 10020.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.168456 restraints weight = 8062.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.169328 restraints weight = 6743.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.170261 restraints weight = 5911.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.4326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5941
moved from start:          0.3854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7278  Z= 0.148
  Angle     :  0.636   9.545  10016  Z= 0.319
  Chirality :  0.045   0.251   1217
  Planarity :  0.005   0.048   1284
  Dihedral  :  6.523  75.474   1115
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 27.08 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.11 (0.28), residues: 987
  helix:  1.16 (1.14), residues: 24
  sheet: -0.67 (0.27), residues: 400
  loop : -0.80 (0.27), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG M  67 
 TYR   0.016   0.002   TYR H  98 
 PHE   0.015   0.001   PHE B 349 
 TRP   0.051   0.003   TRP I  39 
 HIS   0.003   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 7274)
  covalent geometry    : angle       0.63636 (10008)
  SS BOND              : bond        0.00290 (    4)
  SS BOND              : angle       0.71144 (    8)
  hydrogen bonds       : bond        0.02784 (  254)
  hydrogen bonds       : angle       5.88134 (  627)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 133
  time to evaluate  : 0.306 
Fit side-chains
REVERT: B  173 TYR cc_start: 0.5967 (m-80) cc_final: 0.5210 (m-10)
REVERT: B  233 ILE cc_start: 0.0357 (OUTLIER) cc_final: -0.0045 (mt)
REVERT: B  295 HIS cc_start: 0.7053 (OUTLIER) cc_final: 0.6022 (t-90)
REVERT: I   55 SER cc_start: 0.6809 (t) cc_final: 0.6289 (p)
REVERT: I   78 SER cc_start: 0.7656 (m) cc_final: 0.7240 (p)
REVERT: M   49 ILE cc_start: 0.7758 (mt) cc_final: 0.7535 (tt)
REVERT: M   62 ARG cc_start: 0.6028 (ptt90) cc_final: 0.5738 (ptt90)
REVERT: M   90 GLN cc_start: 0.7217 (tm-30) cc_final: 0.6929 (tm-30)
REVERT: A  278 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.6214 (pp)
REVERT: A  320 SER cc_start: 0.7434 (t) cc_final: 0.6928 (p)
REVERT: L   38 GLN cc_start: 0.4773 (tt0) cc_final: 0.4179 (mm-40)
REVERT: L   49 ILE cc_start: 0.7280 (tp) cc_final: 0.6936 (tp)
  outliers start: 36
  outliers final: 28
  residues processed: 154
  average time/residue: 0.0801
  time to fit residues: 16.9499
Evaluate side-chains
  163 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 132
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 ASP
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  229 LYS
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  241 ILE
Chi-restraints excluded: chain B residue  295 HIS
Chi-restraints excluded: chain I residue   51 VAL
Chi-restraints excluded: chain I residue   53 SER
Chi-restraints excluded: chain I residue   54 ILE
Chi-restraints excluded: chain I residue   94 THR
Chi-restraints excluded: chain M residue   34 VAL
Chi-restraints excluded: chain M residue   89 CYS
Chi-restraints excluded: chain M residue   95 VAL
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain A residue   35 ASP
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  229 LYS
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   51 VAL
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   95 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 91 optimal weight:    0.5980
   chunk 69 optimal weight:    0.0070
   chunk 13 optimal weight:    0.3980
   chunk 15 optimal weight:    0.0970
   chunk 25 optimal weight:    0.0060
   chunk 71 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.2212

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

Flipped N/Q/H residues before XYZ refinement:
M  90 GLN
A 237 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.182324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.166645 restraints weight = 13064.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.169095 restraints weight = 9528.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.170890 restraints weight = 7400.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.172206 restraints weight = 6031.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.173187 restraints weight = 5110.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.4365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5867
moved from start:          0.4156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7278  Z= 0.103
  Angle     :  0.610  14.163  10016  Z= 0.299
  Chirality :  0.043   0.191   1217
  Planarity :  0.005   0.050   1284
  Dihedral  :  6.249  77.433   1115
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 28.82 %
    Favored  : 66.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.96 (0.28), residues: 987
  helix:  1.69 (1.18), residues: 24
  sheet: -0.56 (0.26), residues: 408
  loop : -0.73 (0.27), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 282 
 TYR   0.016   0.001   TYR H  62 
 PHE   0.015   0.001   PHE B 349 
 TRP   0.043   0.003   TRP I  39 
 HIS   0.003   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 7274)
  covalent geometry    : angle       0.61015 (10008)
  SS BOND              : bond        0.00280 (    4)
  SS BOND              : angle       0.59275 (    8)
  hydrogen bonds       : bond        0.02333 (  254)
  hydrogen bonds       : angle       5.35370 (  627)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 134
  time to evaluate  : 0.259 
Fit side-chains
REVERT: B  173 TYR cc_start: 0.5857 (m-80) cc_final: 0.5595 (m-80)
REVERT: B  233 ILE cc_start: 0.0171 (OUTLIER) cc_final: -0.0184 (mt)
REVERT: B  295 HIS cc_start: 0.6823 (OUTLIER) cc_final: 0.5962 (t-90)
REVERT: B  320 SER cc_start: 0.7283 (t) cc_final: 0.7041 (p)
REVERT: I   55 SER cc_start: 0.6608 (t) cc_final: 0.6175 (p)
REVERT: I   78 SER cc_start: 0.7661 (m) cc_final: 0.7249 (p)
REVERT: M   49 ILE cc_start: 0.7683 (mt) cc_final: 0.7424 (tt)
REVERT: M   90 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6973 (tm130)
REVERT: M   95 VAL cc_start: 0.7025 (OUTLIER) cc_final: 0.6764 (m)
REVERT: A  278 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6699 (pp)
REVERT: A  320 SER cc_start: 0.7376 (t) cc_final: 0.6880 (p)
REVERT: L   38 GLN cc_start: 0.4564 (tt0) cc_final: 0.4180 (mm-40)
  outliers start: 27
  outliers final: 21
  residues processed: 148
  average time/residue: 0.0786
  time to fit residues: 16.1129
Evaluate side-chains
  157 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  229 LYS
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  295 HIS
Chi-restraints excluded: chain I residue   54 ILE
Chi-restraints excluded: chain I residue   94 THR
Chi-restraints excluded: chain M residue   34 VAL
Chi-restraints excluded: chain M residue   89 CYS
Chi-restraints excluded: chain M residue   90 GLN
Chi-restraints excluded: chain M residue   95 VAL
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  229 LYS
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   81 THR
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   95 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 28 optimal weight:    7.9990
   chunk 77 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 43 optimal weight:    0.3980
   chunk 25 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 237 GLN
L  38 GLN
L  91 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.177580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.163781 restraints weight = 13012.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.165702 restraints weight = 9964.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.167142 restraints weight = 7997.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.168183 restraints weight = 6671.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.169045 restraints weight = 5765.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.4315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5973
moved from start:          0.4115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7278  Z= 0.186
  Angle     :  0.683  11.719  10016  Z= 0.342
  Chirality :  0.046   0.225   1217
  Planarity :  0.005   0.052   1284
  Dihedral  :  6.519  74.639   1115
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 29.17 %
    Favored  : 65.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.10 (0.28), residues: 987
  helix:  1.35 (1.11), residues: 24
  sheet: -0.70 (0.26), residues: 420
  loop : -0.77 (0.28), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG M  67 
 TYR   0.022   0.002   TYR H  98 
 PHE   0.011   0.002   PHE A 277 
 TRP   0.047   0.003   TRP I  39 
 HIS   0.004   0.001   HIS I  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 7274)
  covalent geometry    : angle       0.68329 (10008)
  SS BOND              : bond        0.00376 (    4)
  SS BOND              : angle       0.85727 (    8)
  hydrogen bonds       : bond        0.03026 (  254)
  hydrogen bonds       : angle       5.86626 (  627)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 134
  time to evaluate  : 0.267 
Fit side-chains
REVERT: B  173 TYR cc_start: 0.5866 (m-80) cc_final: 0.5573 (m-80)
REVERT: B  233 ILE cc_start: 0.0496 (OUTLIER) cc_final: 0.0074 (mt)
REVERT: B  295 HIS cc_start: 0.7077 (OUTLIER) cc_final: 0.6144 (t-90)
REVERT: I   55 SER cc_start: 0.6886 (t) cc_final: 0.6550 (p)
REVERT: I   78 SER cc_start: 0.7707 (m) cc_final: 0.7308 (p)
REVERT: M   49 ILE cc_start: 0.7807 (mt) cc_final: 0.7531 (tt)
REVERT: M   90 GLN cc_start: 0.7253 (tm-30) cc_final: 0.6815 (tm-30)
REVERT: M   95 VAL cc_start: 0.7281 (OUTLIER) cc_final: 0.7036 (m)
REVERT: A  278 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6963 (pp)
REVERT: A  320 SER cc_start: 0.7484 (t) cc_final: 0.7015 (p)
REVERT: L   38 GLN cc_start: 0.5011 (tt0) cc_final: 0.4074 (mm-40)
  outliers start: 30
  outliers final: 22
  residues processed: 152
  average time/residue: 0.0752
  time to fit residues: 15.8760
Evaluate side-chains
  159 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 133
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 ASP
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  183 THR
Chi-restraints excluded: chain B residue  229 LYS
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  295 HIS
Chi-restraints excluded: chain I residue   53 SER
Chi-restraints excluded: chain I residue   54 ILE
Chi-restraints excluded: chain I residue   94 THR
Chi-restraints excluded: chain I residue  110 LEU
Chi-restraints excluded: chain M residue   34 VAL
Chi-restraints excluded: chain M residue   51 SER
Chi-restraints excluded: chain M residue   89 CYS
Chi-restraints excluded: chain M residue   95 VAL
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  229 LYS
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   24 SER
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   95 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 8 optimal weight:    0.0980
   chunk 44 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 34 optimal weight:    0.4980
   chunk 73 optimal weight:    0.7980
   chunk 76 optimal weight:    0.2980
   chunk 2 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0970
   overall best weight:    0.3178

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

Flipped N/Q/H residues before XYZ refinement:
A 237 GLN
L  38 GLN
L  91 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.180974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.165499 restraints weight = 13051.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.167914 restraints weight = 9503.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.169669 restraints weight = 7381.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.170967 restraints weight = 6022.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.171945 restraints weight = 5110.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.4349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5897
moved from start:          0.4317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7278  Z= 0.115
  Angle     :  0.615  12.056  10016  Z= 0.304
  Chirality :  0.043   0.189   1217
  Planarity :  0.005   0.049   1284
  Dihedral  :  6.289  76.962   1115
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 30.21 %
    Favored  : 65.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.97 (0.28), residues: 987
  helix:  1.63 (1.15), residues: 24
  sheet: -0.57 (0.26), residues: 410
  loop : -0.74 (0.27), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  25 
 TYR   0.016   0.001   TYR H  62 
 PHE   0.015   0.001   PHE B 349 
 TRP   0.035   0.003   TRP I  39 
 HIS   0.003   0.001   HIS A 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 7274)
  covalent geometry    : angle       0.61534 (10008)
  SS BOND              : bond        0.00237 (    4)
  SS BOND              : angle       0.64329 (    8)
  hydrogen bonds       : bond        0.02419 (  254)
  hydrogen bonds       : angle       5.41363 (  627)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1301.87 seconds
wall clock time: 23 minutes 14.38 seconds (1394.38 seconds total)