Starting phenix.real_space_refine
on Wed Feb 12 14:40:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ydp_33755/02_2025/7ydp_33755.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ydp_33755/02_2025/7ydp_33755.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ydp_33755/02_2025/7ydp_33755.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ydp_33755/02_2025/7ydp_33755.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ydp_33755/02_2025/7ydp_33755.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ydp_33755/02_2025/7ydp_33755.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      55      5.16       5
     C    5100      2.51       5
     N    1392      2.21       5
     O    1481      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8028
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 2106
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 269, 2106
          Classifications: {'peptide': 269}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 5, 'TRANS': 263}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 55
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 35
    Chain: "C"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 433
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "A"
      Number of atoms: 1922
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1922
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "D"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
  Time building chain proxies: 5.18, per 1000 atoms: 0.65
  Number of scatterers: 8028
  At special positions: 0
  Unit cell: (78.1, 97.9, 136.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      55     16.00
     O    1481      8.00
     N    1392      7.00
     C    5100      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 612 " - pdb=" SG  CYS R 684 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.02

  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: 1.83
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1910

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 10 sheets defined
      41.1% alpha, 19.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'R' and resid 532 through 537
    Processing helix  chain 'R' and resid 544 through 572
      removed outlier: 3.511A  pdb=" N   THR R 548 " --> pdb=" O   ASP R 544 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 577 through 601
      removed outlier: 3.640A  pdb=" N   THR R 581 " --> pdb=" O   GLY R 577 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ILE R 601 " --> pdb=" O   PHE R 597 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 609 through 642
      removed outlier: 3.907A  pdb=" N   SER R 631 " --> pdb=" O   PHE R 627 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 652 through 669
      Proline residue:  R 663  - end of helix
    Processing helix  chain 'R' and resid 688 through 695
      removed outlier: 6.082A  pdb=" N   LEU R 693 " --> pdb=" O   GLN R 690 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   TRP R 694 " --> pdb=" O   GLY R 691 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   SER R 695 " --> pdb=" O   PHE R 692 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 697 through 726
      removed outlier: 3.587A  pdb=" N   SER R 723 " --> pdb=" O   THR R 719 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   GLU R 724 " --> pdb=" O   GLN R 720 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ASN R 726 " --> pdb=" O   PHE R 722 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 730 through 749
    Processing helix  chain 'R' and resid 751 through 758
    Processing helix  chain 'R' and resid 764 through 775
    Processing helix  chain 'R' and resid 777 through 786
    Processing helix  chain 'R' and resid 790 through 802
      removed outlier: 3.909A  pdb=" N   GLU R 795 " --> pdb=" O   LYS R 791 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   GLU R 796 " --> pdb=" O   LYS R 792 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   ARG R 798 " --> pdb=" O   ARG R 794 " (cutoff:3.500A)
      removed outlier: 4.704A  pdb=" N   LYS R 799 " --> pdb=" O   GLU R 795 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 9 through 24
      removed outlier: 3.748A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 42
      removed outlier: 3.860A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 48
      removed outlier: 3.504A  pdb=" N   GLU C  47 " --> pdb=" O   HIS C  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 13 through 40
      removed outlier: 4.362A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   THR A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
    Processing helix  chain 'A' and resid 235 through 239
      removed outlier: 3.528A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.745A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 318
      removed outlier: 3.759A  pdb=" N   PHE A 315 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   TYR A 318 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.576A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.966A  pdb=" N   ARG A 374 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   ARG A 389 " --> pdb=" O   ARG A 385 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 28 through 32
      removed outlier: 3.812A  pdb=" N   ASN D  31 " --> pdb=" O   THR D  28 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   TYR D  32 " --> pdb=" O   PHE D  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 28 through 32'
    Processing helix  chain 'D' and resid 61 through 65
    Processing helix  chain 'D' and resid 87 through 91
      removed outlier: 4.068A  pdb=" N   THR D  91 " --> pdb=" O   PRO D  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.695A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.622A  pdb=" N   PHE A 222 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   LEU A  45 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.387A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.564A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.980A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 9.018A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 5.933A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.589A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 7
    Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.019A  pdb=" N   GLY D  10 " --> pdb=" O   THR D 125 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ARG D  38 " --> pdb=" O   TRP D  47 " (cutoff:3.500A)
      removed outlier: 5.406A  pdb=" N   TRP D  47 " --> pdb=" O   ARG D  38 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ASP D  50 " --> pdb=" O   SER D  59 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   SER D  59 " --> pdb=" O   ASP D  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51
      removed outlier: 7.296A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 5.386A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 60
      removed outlier: 7.160A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.521A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.794A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.870A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153
      removed outlier: 7.197A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.443A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.380A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.117A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.483A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 232
      removed outlier: 6.695A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.962A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    382 hydrogen bonds defined for protein.
    1047 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: 2.39

  Time building geometry restraints manager: 2.14 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2557
        1.34 -     1.45: 1270
        1.45 -     1.57: 4292
        1.57 -     1.69: 0
        1.69 -     1.81: 73
  Bond restraints: 8192
  Sorted by residual:
  bond pdb=" C   ARG D  98 "
       pdb=" N   CYS D  99 "
    ideal  model  delta    sigma   weight residual
    1.340  1.234  0.106 5.87e-02 2.90e+02 3.28e+00
  bond pdb=" CA  SER B  67 "
       pdb=" C   SER B  67 "
    ideal  model  delta    sigma   weight residual
    1.524  1.501  0.023 1.59e-02 3.96e+03 2.10e+00
  bond pdb=" CB  TRP D  36 "
       pdb=" CG  TRP D  36 "
    ideal  model  delta    sigma   weight residual
    1.498  1.458  0.040 3.10e-02 1.04e+03 1.64e+00
  bond pdb=" CG  LEU R 619 "
       pdb=" CD2 LEU R 619 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.50e+00
  bond pdb=" CA  ASN B 313 "
       pdb=" CB  ASN B 313 "
    ideal  model  delta    sigma   weight residual
    1.538  1.525  0.013 1.22e-02 6.72e+03 1.10e+00
  ... (remaining 8187 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 10580
        1.56 -     3.12: 438
        3.12 -     4.68: 57
        4.68 -     6.24: 16
        6.24 -     7.80: 5
  Bond angle restraints: 11096
  Sorted by residual:
  angle pdb=" N   ILE B 270 "
        pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
      ideal   model   delta    sigma   weight residual
     112.43  108.48    3.95 9.20e-01 1.18e+00 1.84e+01
  angle pdb=" N   GLY R 600 "
        pdb=" CA  GLY R 600 "
        pdb=" C   GLY R 600 "
      ideal   model   delta    sigma   weight residual
     115.80  123.07   -7.27 1.74e+00 3.30e-01 1.74e+01
  angle pdb=" C   TYR B 105 "
        pdb=" N   ALA B 106 "
        pdb=" CA  ALA B 106 "
      ideal   model   delta    sigma   weight residual
     120.68  125.97   -5.29 1.52e+00 4.33e-01 1.21e+01
  angle pdb=" CA  SER B  67 "
        pdb=" C   SER B  67 "
        pdb=" N   ARG B  68 "
      ideal   model   delta    sigma   weight residual
     117.92  113.86    4.06 1.35e+00 5.49e-01 9.05e+00
  angle pdb=" CA  TYR B 105 "
        pdb=" CB  TYR B 105 "
        pdb=" CG  TYR B 105 "
      ideal   model   delta    sigma   weight residual
     113.90  119.07   -5.17 1.80e+00 3.09e-01 8.26e+00
  ... (remaining 11091 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.67: 4434
       16.67 -    33.34: 343
       33.34 -    50.01: 60
       50.01 -    66.69: 9
       66.69 -    83.36: 6
  Dihedral angle restraints: 4852
    sinusoidal: 1893
      harmonic: 2959
  Sorted by residual:
  dihedral pdb=" CA  PHE D 108 "
           pdb=" C   PHE D 108 "
           pdb=" N   ASP D 109 "
           pdb=" CA  ASP D 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.10   25.90     0      5.00e+00 4.00e-02 2.68e+01
  dihedral pdb=" CB  CYS R 612 "
           pdb=" SG  CYS R 612 "
           pdb=" SG  CYS R 684 "
           pdb=" CB  CYS R 684 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -127.49   41.49     1      1.00e+01 1.00e-02 2.41e+01
  dihedral pdb=" CB  CYS D  22 "
           pdb=" SG  CYS D  22 "
           pdb=" SG  CYS D  96 "
           pdb=" CB  CYS D  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -45.94  -40.06     1      1.00e+01 1.00e-02 2.25e+01
  ... (remaining 4849 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 747
       0.035 -    0.071: 340
       0.071 -    0.106: 120
       0.106 -    0.142: 43
       0.142 -    0.177: 5
  Chirality restraints: 1255
  Sorted by residual:
  chirality pdb=" CA  GLN R 745 "
            pdb=" N   GLN R 745 "
            pdb=" C   GLN R 745 "
            pdb=" CB  GLN R 745 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.85e-01
  chirality pdb=" CA  ILE B 273 "
            pdb=" N   ILE B 273 "
            pdb=" C   ILE B 273 "
            pdb=" CB  ILE B 273 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.48e-01
  chirality pdb=" CG  LEU R 598 "
            pdb=" CB  LEU R 598 "
            pdb=" CD1 LEU R 598 "
            pdb=" CD2 LEU R 598 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.63e-01
  ... (remaining 1252 not shown)

  Planarity restraints: 1411
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA D 101 "    0.040 5.00e-02 4.00e+02   6.13e-02 6.01e+00
        pdb=" N   PRO D 102 "   -0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO D 102 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO D 102 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG R 680 "   -0.035 5.00e-02 4.00e+02   5.23e-02 4.38e+00
        pdb=" N   PRO R 681 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO R 681 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO R 681 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA D  40 "   -0.031 5.00e-02 4.00e+02   4.79e-02 3.67e+00
        pdb=" N   PRO D  41 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO D  41 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO D  41 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1408 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 156
        2.68 -     3.23: 7593
        3.23 -     3.79: 11885
        3.79 -     4.34: 15680
        4.34 -     4.90: 26132
  Nonbonded interactions: 61446
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 330 "
            pdb=" OG1 THR A 335 "
     model   vdw
     2.123 3.040
  nonbonded pdb=" OD1 ASP B 212 "
            pdb=" N   VAL B 213 "
     model   vdw
     2.172 3.120
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OE1 GLU B 130 "
            pdb=" NH2 ARG B 134 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" OG1 THR B  34 "
            pdb=" O   LEU B 300 "
     model   vdw
     2.258 3.040
  ... (remaining 61441 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.730
  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:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.400
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6223
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.106   8192  Z= 0.315
  Angle     :  0.733   7.803  11096  Z= 0.431
  Chirality :  0.047   0.177   1255
  Planarity :  0.005   0.061   1411
  Dihedral  : 12.575  83.357   2936
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.25), residues: 1008
  helix:  0.57 (0.27), residues: 362
  sheet: -0.16 (0.35), residues: 182
  loop : -2.25 (0.26), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  82 
 HIS   0.007   0.001   HIS R 583 
 PHE   0.030   0.003   PHE B 151 
 TYR   0.022   0.002   TYR B 124 
 ARG   0.007   0.000   ARG B  48 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 MET cc_start: 0.5104 (mmp) cc_final: 0.4792 (mmt)
REVERT: B   59 TYR cc_start: 0.4344 (p90) cc_final: 0.3897 (p90)
REVERT: B  102 THR cc_start: 0.6778 (t) cc_final: 0.5467 (m)
REVERT: B  217 MET cc_start: 0.6210 (tmm) cc_final: 0.5989 (tmm)
REVERT: B  297 TRP cc_start: 0.7084 (m100) cc_final: 0.6784 (m100)
REVERT: B  304 ARG cc_start: 0.6952 (ttp-170) cc_final: 0.6455 (ttp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.2223
  time to fit residues: 42.9757
Evaluate side-chains
  136 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    0.5980
   chunk 75 optimal weight:    0.2980
   chunk 41 optimal weight:    0.0770
   chunk 25 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 30 optimal weight:    0.2980
   chunk 47 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.4138

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

Flipped N/Q/H residues before XYZ refinement:
R 576 GLN
** R 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
B 239 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.186187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.161139 restraints weight = 10992.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.4139 rms_B_bonded: 2.39
r_work: 0.4032 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.4032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6364
moved from start:          0.1061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8192  Z= 0.200
  Angle     :  0.623  10.700  11096  Z= 0.337
  Chirality :  0.043   0.149   1255
  Planarity :  0.005   0.055   1411
  Dihedral  :  5.319  23.108   1112
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  7.29 %
    Favored  : 91.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.26), residues: 1008
  helix:  0.99 (0.28), residues: 372
  sheet:  0.06 (0.33), residues: 208
  loop : -2.03 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 297 
 HIS   0.006   0.001   HIS R 583 
 PHE   0.019   0.002   PHE A 212 
 TYR   0.018   0.002   TYR B 124 
 ARG   0.004   0.000   ARG B  49 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 131
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  576 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7404 (mp10)
REVERT: R  783 TYR cc_start: 0.6840 (t80) cc_final: 0.5990 (t80)
REVERT: A  350 THR cc_start: 0.7989 (t) cc_final: 0.7611 (t)
REVERT: A  386 MET cc_start: 0.6096 (mmp) cc_final: 0.5604 (mmt)
REVERT: B   59 TYR cc_start: 0.4685 (p90) cc_final: 0.4140 (p90)
REVERT: B  102 THR cc_start: 0.6859 (t) cc_final: 0.5558 (m)
REVERT: B  217 MET cc_start: 0.6758 (tmm) cc_final: 0.6401 (tmm)
REVERT: B  219 ARG cc_start: 0.7450 (mtp85) cc_final: 0.7237 (mtp85)
REVERT: B  297 TRP cc_start: 0.7435 (m100) cc_final: 0.6511 (m100)
  outliers start: 8
  outliers final: 4
  residues processed: 136
  average time/residue: 0.2268
  time to fit residues: 41.3908
Evaluate side-chains
  131 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 126
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  559 LEU
Chi-restraints excluded: chain R residue  576 GLN
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain B residue  273 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 72 optimal weight:    0.0980
   chunk 37 optimal weight:    0.0470
   chunk 55 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 64 optimal weight:    0.0070
   chunk 94 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.3896

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

Flipped N/Q/H residues before XYZ refinement:
** R 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 213 GLN
B 110 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.186624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.161333 restraints weight = 11242.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.4139 rms_B_bonded: 2.43
r_work: 0.4033 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6355
moved from start:          0.1443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8192  Z= 0.179
  Angle     :  0.574  10.301  11096  Z= 0.315
  Chirality :  0.042   0.146   1255
  Planarity :  0.004   0.054   1411
  Dihedral  :  5.014  21.308   1112
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  9.38 %
    Favored  : 89.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.26), residues: 1008
  helix:  1.24 (0.28), residues: 373
  sheet:  0.14 (0.33), residues: 210
  loop : -1.89 (0.28), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 297 
 HIS   0.009   0.001   HIS R 786 
 PHE   0.020   0.001   PHE A 212 
 TYR   0.017   0.002   TYR R 678 
 ARG   0.004   0.000   ARG B  49 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 133
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
REVERT: R  576 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7354 (mp-120)
REVERT: R  729 MET cc_start: 0.1539 (ttp) cc_final: 0.1312 (ttp)
REVERT: R  745 GLN cc_start: 0.6920 (mp10) cc_final: 0.6533 (mp10)
REVERT: R  783 TYR cc_start: 0.6862 (t80) cc_final: 0.6122 (t80)
REVERT: A   60 MET cc_start: 0.5256 (OUTLIER) cc_final: 0.5003 (mtm)
REVERT: A  221 MET cc_start: 0.7079 (mtt) cc_final: 0.6765 (mtp)
REVERT: A  283 ARG cc_start: 0.7508 (mtm110) cc_final: 0.7308 (mtm110)
REVERT: A  350 THR cc_start: 0.7936 (t) cc_final: 0.7587 (t)
REVERT: A  386 MET cc_start: 0.6102 (mmp) cc_final: 0.5578 (mmt)
REVERT: B   45 MET cc_start: 0.7650 (mtm) cc_final: 0.6990 (ptp)
REVERT: B   49 ARG cc_start: 0.7735 (mmm-85) cc_final: 0.7323 (mtp85)
REVERT: B   59 TYR cc_start: 0.4634 (p90) cc_final: 0.4037 (p90)
REVERT: B  101 MET cc_start: 0.6124 (mtt) cc_final: 0.5393 (mtt)
REVERT: B  102 THR cc_start: 0.6979 (t) cc_final: 0.5599 (m)
REVERT: B  262 MET cc_start: 0.5961 (tmm) cc_final: 0.5547 (tmm)
REVERT: B  307 VAL cc_start: 0.8533 (t) cc_final: 0.8307 (m)
  outliers start: 9
  outliers final: 5
  residues processed: 136
  average time/residue: 0.2325
  time to fit residues: 42.1531
Evaluate side-chains
  135 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 128
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  559 LEU
Chi-restraints excluded: chain R residue  576 GLN
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  378 ASP
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  273 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 44 optimal weight:    0.4980
   chunk 9 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
R 576 GLN
** R 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 213 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.183177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.157168 restraints weight = 11112.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.4133 rms_B_bonded: 2.56
r_work: 0.4028 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6396
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   8192  Z= 0.241
  Angle     :  0.597  10.528  11096  Z= 0.325
  Chirality :  0.044   0.245   1255
  Planarity :  0.004   0.054   1411
  Dihedral  :  5.035  22.997   1112
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 11.34 %
    Favored  : 86.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.26), residues: 1008
  helix:  1.24 (0.28), residues: 375
  sheet:  0.25 (0.34), residues: 209
  loop : -1.85 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  82 
 HIS   0.007   0.001   HIS R 786 
 PHE   0.024   0.002   PHE A 212 
 TYR   0.017   0.002   TYR B 124 
 ARG   0.004   0.000   ARG B  49 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 1.021 
Fit side-chains
   revert: symmetry clash
REVERT: R  745 GLN cc_start: 0.6891 (mp10) cc_final: 0.6582 (mp10)
REVERT: R  783 TYR cc_start: 0.6911 (t80) cc_final: 0.6287 (t80)
REVERT: A   60 MET cc_start: 0.5201 (OUTLIER) cc_final: 0.4805 (mtm)
REVERT: A  350 THR cc_start: 0.8000 (t) cc_final: 0.7701 (t)
REVERT: A  386 MET cc_start: 0.6086 (mmp) cc_final: 0.5570 (mmt)
REVERT: B   45 MET cc_start: 0.7657 (mtm) cc_final: 0.7291 (ptp)
REVERT: B   49 ARG cc_start: 0.7730 (mmm-85) cc_final: 0.7407 (mtp85)
REVERT: B   59 TYR cc_start: 0.4642 (p90) cc_final: 0.4140 (p90)
REVERT: B  102 THR cc_start: 0.6964 (t) cc_final: 0.5515 (m)
  outliers start: 19
  outliers final: 9
  residues processed: 136
  average time/residue: 0.2338
  time to fit residues: 42.1394
Evaluate side-chains
  136 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  541 ASP
Chi-restraints excluded: chain R residue  559 LEU
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  285 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0050
   chunk 43 optimal weight:    0.4980
   chunk 46 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 87 optimal weight:    3.9990
   chunk 52 optimal weight:    0.3980
   chunk 96 optimal weight:    0.0870
   overall best weight:    0.3172

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

Flipped N/Q/H residues before XYZ refinement:
** R 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.188429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.162089 restraints weight = 11087.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.4167 rms_B_bonded: 2.59
r_work: 0.4060 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.4060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6353
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8192  Z= 0.159
  Angle     :  0.556  11.058  11096  Z= 0.300
  Chirality :  0.042   0.230   1255
  Planarity :  0.004   0.054   1411
  Dihedral  :  4.745  21.755   1112
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.50 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.26), residues: 1008
  helix:  1.40 (0.28), residues: 376
  sheet:  0.44 (0.34), residues: 205
  loop : -1.77 (0.28), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R 583 
 PHE   0.016   0.001   PHE A 212 
 TYR   0.016   0.001   TYR B 124 
 ARG   0.003   0.000   ARG B  49 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
REVERT: R  783 TYR cc_start: 0.6873 (t80) cc_final: 0.6293 (t80)
REVERT: A   60 MET cc_start: 0.4994 (OUTLIER) cc_final: 0.4717 (ptp)
REVERT: A  350 THR cc_start: 0.7940 (t) cc_final: 0.7615 (t)
REVERT: A  386 MET cc_start: 0.6125 (mmp) cc_final: 0.5626 (mmt)
REVERT: B   45 MET cc_start: 0.7630 (mtm) cc_final: 0.7298 (ptp)
REVERT: B   49 ARG cc_start: 0.7687 (mmm-85) cc_final: 0.7410 (mtp85)
REVERT: B   59 TYR cc_start: 0.4682 (p90) cc_final: 0.4243 (p90)
REVERT: B  102 THR cc_start: 0.6949 (t) cc_final: 0.5561 (m)
REVERT: B  297 TRP cc_start: 0.7476 (m100) cc_final: 0.6592 (m100)
  outliers start: 18
  outliers final: 10
  residues processed: 140
  average time/residue: 0.2308
  time to fit residues: 42.8196
Evaluate side-chains
  140 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  559 LEU
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  378 ASP
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  285 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 96 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 95 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** R 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.183949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.157799 restraints weight = 11017.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.4136 rms_B_bonded: 2.56
r_work: 0.4031 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.4031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6414
moved from start:          0.1838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   8192  Z= 0.271
  Angle     :  0.623  11.515  11096  Z= 0.331
  Chirality :  0.044   0.202   1255
  Planarity :  0.005   0.053   1411
  Dihedral  :  4.925  23.654   1112
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 13.89 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.26), residues: 1008
  helix:  1.30 (0.27), residues: 376
  sheet:  0.47 (0.35), residues: 202
  loop : -1.84 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 169 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.026   0.002   PHE B 199 
 TYR   0.018   0.002   TYR B 124 
 ARG   0.014   0.000   ARG A 283 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
REVERT: R  783 TYR cc_start: 0.6907 (t80) cc_final: 0.6447 (t80)
REVERT: A  386 MET cc_start: 0.6073 (mmp) cc_final: 0.5591 (mmt)
REVERT: B   45 MET cc_start: 0.7631 (mtm) cc_final: 0.7346 (ptp)
REVERT: B   49 ARG cc_start: 0.7722 (mmm-85) cc_final: 0.7363 (mtp85)
REVERT: B   59 TYR cc_start: 0.4579 (p90) cc_final: 0.4160 (p90)
REVERT: B  297 TRP cc_start: 0.7522 (m100) cc_final: 0.6931 (m100)
  outliers start: 17
  outliers final: 14
  residues processed: 125
  average time/residue: 0.2366
  time to fit residues: 38.7233
Evaluate side-chains
  130 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  541 ASP
Chi-restraints excluded: chain R residue  559 LEU
Chi-restraints excluded: chain R residue  748 LEU
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  285 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 41 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 90 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0670
   chunk 77 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
** R 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.185780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.159577 restraints weight = 11073.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.4134 rms_B_bonded: 2.58
r_work: 0.4029 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.4029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6367
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   8192  Z= 0.242
  Angle     :  0.603  11.813  11096  Z= 0.323
  Chirality :  0.044   0.214   1255
  Planarity :  0.005   0.059   1411
  Dihedral  :  4.872  23.652   1112
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 14.12 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.26), residues: 1008
  helix:  1.38 (0.27), residues: 375
  sheet:  0.44 (0.35), residues: 202
  loop : -1.79 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.023   0.002   PHE B 199 
 TYR   0.017   0.002   TYR B 124 
 ARG   0.014   0.000   ARG A 283 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
REVERT: R  783 TYR cc_start: 0.6876 (t80) cc_final: 0.6420 (t80)
REVERT: A  350 THR cc_start: 0.7943 (t) cc_final: 0.7636 (t)
REVERT: A  386 MET cc_start: 0.6100 (mmp) cc_final: 0.5625 (mmt)
REVERT: B   45 MET cc_start: 0.7698 (mtm) cc_final: 0.7381 (ptp)
REVERT: B   49 ARG cc_start: 0.7755 (mmm-85) cc_final: 0.7394 (mtp85)
REVERT: B   59 TYR cc_start: 0.4496 (p90) cc_final: 0.4017 (p90)
REVERT: B  234 PHE cc_start: 0.6105 (OUTLIER) cc_final: 0.5041 (m-80)
REVERT: B  297 TRP cc_start: 0.7501 (m100) cc_final: 0.6907 (m100)
  outliers start: 15
  outliers final: 12
  residues processed: 122
  average time/residue: 0.2597
  time to fit residues: 41.9577
Evaluate side-chains
  125 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  541 ASP
Chi-restraints excluded: chain R residue  559 LEU
Chi-restraints excluded: chain R residue  748 LEU
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  285 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 27 optimal weight:    9.9990
   chunk 66 optimal weight:   20.0000
   chunk 44 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0370
   chunk 47 optimal weight:    0.5980
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
** R 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.184672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.158610 restraints weight = 11045.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.4135 rms_B_bonded: 2.58
r_work: 0.4026 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.4026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6369
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8192  Z= 0.225
  Angle     :  0.599  11.989  11096  Z= 0.319
  Chirality :  0.043   0.206   1255
  Planarity :  0.004   0.061   1411
  Dihedral  :  4.798  23.477   1112
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 13.89 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.26), residues: 1008
  helix:  1.45 (0.27), residues: 375
  sheet:  0.48 (0.35), residues: 202
  loop : -1.75 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R 786 
 PHE   0.021   0.002   PHE B 199 
 TYR   0.016   0.002   TYR B 124 
 ARG   0.014   0.000   ARG A 283 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
REVERT: R  783 TYR cc_start: 0.6777 (t80) cc_final: 0.6335 (t80)
REVERT: A  386 MET cc_start: 0.6114 (mmp) cc_final: 0.5660 (mmt)
REVERT: B   45 MET cc_start: 0.7719 (mtm) cc_final: 0.7407 (ptp)
REVERT: B   49 ARG cc_start: 0.7728 (mmm-85) cc_final: 0.7414 (mtp85)
REVERT: B   59 TYR cc_start: 0.4571 (p90) cc_final: 0.4087 (p90)
REVERT: B  219 ARG cc_start: 0.7450 (mtp85) cc_final: 0.7218 (mtp85)
REVERT: B  234 PHE cc_start: 0.6057 (OUTLIER) cc_final: 0.4989 (m-80)
REVERT: B  297 TRP cc_start: 0.7499 (m100) cc_final: 0.6897 (m100)
  outliers start: 17
  outliers final: 13
  residues processed: 128
  average time/residue: 0.2347
  time to fit residues: 40.0395
Evaluate side-chains
  127 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  559 LEU
Chi-restraints excluded: chain R residue  748 LEU
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  285 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 92 optimal weight:    0.4980
   chunk 78 optimal weight:    1.9990
   chunk 55 optimal weight:    0.4980
   chunk 93 optimal weight:    0.9980
   chunk 60 optimal weight:    0.4980
   chunk 80 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** R 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.185617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.159367 restraints weight = 11212.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.4143 rms_B_bonded: 2.61
r_work: 0.4035 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.4035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6386
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   8192  Z= 0.229
  Angle     :  0.618  12.959  11096  Z= 0.329
  Chirality :  0.044   0.206   1255
  Planarity :  0.005   0.070   1411
  Dihedral  :  4.791  23.357   1112
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 14.47 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.27), residues: 1008
  helix:  1.48 (0.27), residues: 375
  sheet:  0.44 (0.36), residues: 202
  loop : -1.74 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.009   0.001   HIS A 220 
 PHE   0.021   0.002   PHE B 199 
 TYR   0.017   0.002   TYR B 124 
 ARG   0.016   0.000   ARG A 283 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
REVERT: A  386 MET cc_start: 0.6060 (mmp) cc_final: 0.5632 (mmt)
REVERT: B   45 MET cc_start: 0.7691 (mtm) cc_final: 0.7416 (ptp)
REVERT: B   49 ARG cc_start: 0.7683 (mmm-85) cc_final: 0.7418 (mtp85)
REVERT: B   59 TYR cc_start: 0.4624 (p90) cc_final: 0.4156 (p90)
REVERT: B  102 THR cc_start: 0.6992 (t) cc_final: 0.5623 (m)
REVERT: B  219 ARG cc_start: 0.7486 (mtp85) cc_final: 0.7257 (mtp85)
REVERT: B  234 PHE cc_start: 0.6053 (OUTLIER) cc_final: 0.5023 (m-80)
REVERT: B  297 TRP cc_start: 0.7522 (m100) cc_final: 0.6909 (m100)
  outliers start: 18
  outliers final: 14
  residues processed: 126
  average time/residue: 0.2310
  time to fit residues: 38.7043
Evaluate side-chains
  128 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  541 ASP
Chi-restraints excluded: chain R residue  559 LEU
Chi-restraints excluded: chain R residue  748 LEU
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  320 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 87 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** R 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.183243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.157037 restraints weight = 11108.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.4122 rms_B_bonded: 2.58
r_work: 0.4015 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6428
moved from start:          0.2073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087   8192  Z= 0.286
  Angle     :  0.647  12.423  11096  Z= 0.346
  Chirality :  0.045   0.204   1255
  Planarity :  0.005   0.073   1411
  Dihedral  :  4.971  25.259   1112
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 14.35 %
    Favored  : 83.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.26), residues: 1008
  helix:  1.38 (0.27), residues: 376
  sheet:  0.36 (0.35), residues: 202
  loop : -1.80 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 169 
 HIS   0.009   0.001   HIS A 220 
 PHE   0.026   0.002   PHE B 199 
 TYR   0.018   0.002   TYR B 124 
 ARG   0.017   0.000   ARG A 283 

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 MET cc_start: 0.6079 (mmp) cc_final: 0.5643 (mmt)
REVERT: B   45 MET cc_start: 0.7633 (mtm) cc_final: 0.7377 (ptp)
REVERT: B   49 ARG cc_start: 0.7642 (mmm-85) cc_final: 0.7396 (mtp85)
REVERT: B   59 TYR cc_start: 0.4644 (p90) cc_final: 0.4172 (p90)
REVERT: B  234 PHE cc_start: 0.6252 (OUTLIER) cc_final: 0.5249 (m-80)
REVERT: B  297 TRP cc_start: 0.7541 (m100) cc_final: 0.6963 (m100)
  outliers start: 17
  outliers final: 15
  residues processed: 124
  average time/residue: 0.2386
  time to fit residues: 39.5374
Evaluate side-chains
  128 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  541 ASP
Chi-restraints excluded: chain R residue  559 LEU
Chi-restraints excluded: chain R residue  748 LEU
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   70 ILE
Chi-restraints excluded: chain D residue  110 VAL
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  320 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0170
   chunk 66 optimal weight:   40.0000
   chunk 46 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 93 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.7418

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

Flipped N/Q/H residues before XYZ refinement:
** R 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.183954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.157971 restraints weight = 11157.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.4126 rms_B_bonded: 2.58
r_work: 0.4017 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.4017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6410
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   8192  Z= 0.272
  Angle     :  0.633  10.555  11096  Z= 0.340
  Chirality :  0.044   0.196   1255
  Planarity :  0.005   0.071   1411
  Dihedral  :  4.937  23.889   1112
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 14.70 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.26), residues: 1008
  helix:  1.35 (0.27), residues: 378
  sheet:  0.34 (0.35), residues: 201
  loop : -1.79 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R 786 
 PHE   0.025   0.002   PHE B 199 
 TYR   0.018   0.002   TYR B 124 
 ARG   0.017   0.000   ARG A 283 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5852.34 seconds
wall clock time: 103 minutes 52.76 seconds (6232.76 seconds total)