Starting phenix.real_space_refine
on Sat Dec 28 15:44:06 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ydj_33749/12_2024/7ydj_33749.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ydj_33749/12_2024/7ydj_33749.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ydj_33749/12_2024/7ydj_33749.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ydj_33749/12_2024/7ydj_33749.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ydj_33749/12_2024/7ydj_33749.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ydj_33749/12_2024/7ydj_33749.cif"
  }
  resolution = 3.03
  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=   0.021
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      60      5.16       5
     C    5589      2.51       5
     N    1507      2.21       5
     O    1595      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 8751
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1744
          Classifications: {'peptide': 211}
          Link IDs: {'PTRANS': 4, 'TRANS': 206}
          Chain breaks: 3
    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}
    Chain: "E"
      Number of atoms: 1777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1777
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "R"
      Number of atoms: 2194
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2194
          Classifications: {'peptide': 274}
          Link IDs: {'PTRANS': 5, 'TRANS': 268}
  Time building chain proxies: 4.78, per 1000 atoms: 0.55
  Number of scatterers: 8751
  At special positions: 0
  Unit cell: (92.4, 119.9, 135.3, 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      60     16.00
     O    1595      8.00
     N    1507      7.00
     C    5589      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.05
    Simple disulfide: pdb=" SG  CYS R 612 " - pdb=" SG  CYS R 684 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.01
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2068

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 12 sheets defined
      38.1% alpha, 21.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 38
      removed outlier: 3.840A  pdb=" N   SER A  23 " --> pdb=" O   ALA A  19 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A  31 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ALA A  36 " --> pdb=" O   ARG A  32 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ARG A  38 " --> pdb=" O   ARG A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 65
    Processing helix  chain 'A' and resid 230 through 235
    Processing helix  chain 'A' and resid 236 through 238
      No H-bonds generated for 'chain 'A' and resid 236 through 238'
    Processing helix  chain 'A' and resid 255 through 268
      removed outlier: 3.611A  pdb=" N   SER A 259 " --> pdb=" O   ARG A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 273
      removed outlier: 3.586A  pdb=" N   PHE A 272 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   PHE A 273 " --> pdb=" O   LYS A 270 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 269 through 273'
    Processing helix  chain 'A' and resid 283 through 293
      removed outlier: 3.838A  pdb=" N   LEU A 287 " --> pdb=" O   LYS A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 311
      No H-bonds generated for 'chain 'A' and resid 309 through 311'
    Processing helix  chain 'A' and resid 312 through 323
      removed outlier: 3.755A  pdb=" N   TYR A 316 " --> pdb=" O   ASP A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 364
      removed outlier: 4.228A  pdb=" N   ASN A 344 " --> pdb=" O   ILE A 340 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   LYS A 362 " --> pdb=" O   GLN A 358 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ASP A 363 " --> pdb=" O   GLU A 359 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ILE A 364 " --> pdb=" O   ASN A 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 4.085A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.677A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.623A  pdb=" N   PHE E  32 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 4.184A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'G' and resid 7 through 23
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.914A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 55 through 59
      removed outlier: 3.646A  pdb=" N   ASN G  59 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 532 through 537
    Processing helix  chain 'R' and resid 544 through 572
    Processing helix  chain 'R' and resid 577 through 600
    Processing helix  chain 'R' and resid 609 through 642
      removed outlier: 3.888A  pdb=" N   ARG R 613 " --> pdb=" O   GLY R 609 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 651 through 674
      removed outlier: 3.836A  pdb=" N   VAL R 662 " --> pdb=" O   ILE R 658 " (cutoff:3.500A)
      Proline residue:  R 663  - end of helix
      removed outlier: 3.515A  pdb=" N   TYR R 674 " --> pdb=" O   SER R 670 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 675 through 678
      removed outlier: 4.009A  pdb=" N   TYR R 678 " --> pdb=" O   SER R 675 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 675 through 678'
    Processing helix  chain 'R' and resid 688 through 692
      removed outlier: 3.514A  pdb=" N   GLY R 691 " --> pdb=" O   PHE R 688 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 693 through 726
      removed outlier: 3.695A  pdb=" N   LEU R 697 " --> pdb=" O   LEU R 693 " (cutoff:3.500A)
      Proline residue:  R 699  - end of helix
      removed outlier: 3.532A  pdb=" N   PHE R 702 " --> pdb=" O   GLY R 698 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   CYS R 706 " --> pdb=" O   PHE R 702 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   VAL R 709 " --> pdb=" O   LEU R 705 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   VAL R 712 " --> pdb=" O   ALA R 708 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   SER R 723 " --> pdb=" O   THR R 719 " (cutoff:3.500A)
      removed outlier: 5.918A  pdb=" N   GLU R 724 " --> pdb=" O   GLN R 720 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 730 through 749
      removed outlier: 3.794A  pdb=" N   THR R 739 " --> pdb=" O   ALA R 735 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   PHE R 747 " --> pdb=" O   ILE R 743 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   LEU R 748 " --> pdb=" O   ALA R 744 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU R 749 " --> pdb=" O   GLN R 745 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 754 through 759
      removed outlier: 3.932A  pdb=" N   ILE R 759 " --> pdb=" O   GLY R 756 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 764 through 776
      removed outlier: 3.540A  pdb=" N   THR R 768 " --> pdb=" O   SER R 764 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 777 through 787
    Processing helix  chain 'R' and resid 790 through 804
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213
      removed outlier: 6.261A  pdb=" N   VAL A  41 " --> pdb=" O   LYS A 220 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   SER A 243 " --> pdb=" O   LYS A  42 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   PHE A 333 " --> pdb=" O   ILE A 277 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 6.936A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.834A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.027A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.838A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.089A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.302A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.953A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.984A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.996A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.839A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 7.097A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.856A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7
      removed outlier: 7.133A  pdb=" N   GLY E  16 " --> pdb=" O   SER E  85 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.296A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.281A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 129 through 130
    Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136
      removed outlier: 6.274A  pdb=" N   VAL E 135 " --> pdb=" O   GLU E 234 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   LEU E 166 " --> pdb=" O   LEU E 175 " (cutoff:3.500A)
      removed outlier: 5.844A  pdb=" N   LEU E 175 " --> pdb=" O   LEU E 166 " (cutoff:3.500A)

    405 hydrogen bonds defined for protein.
    1146 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: 2.73

  Time building geometry restraints manager: 2.36 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: 2821
        1.34 -     1.46: 2189
        1.46 -     1.59: 3836
        1.59 -     1.71: 0
        1.71 -     1.83: 85
  Bond restraints: 8931
  Sorted by residual:
  bond pdb=" CB  PRO E 224 "
       pdb=" CG  PRO E 224 "
    ideal  model  delta    sigma   weight residual
    1.506  1.453  0.053 3.90e-02 6.57e+02 1.88e+00
  bond pdb=" SD  MET E 218 "
       pdb=" CE  MET E 218 "
    ideal  model  delta    sigma   weight residual
    1.791  1.760  0.031 2.50e-02 1.60e+03 1.49e+00
  bond pdb=" CB  TRP R 716 "
       pdb=" CG  TRP R 716 "
    ideal  model  delta    sigma   weight residual
    1.498  1.461  0.037 3.10e-02 1.04e+03 1.45e+00
  bond pdb=" CG  LEU R 562 "
       pdb=" CD2 LEU R 562 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.21e+00
  bond pdb=" C   ASP A 306 "
       pdb=" N   PRO A 307 "
    ideal  model  delta    sigma   weight residual
    1.339  1.375 -0.036 3.40e-02 8.65e+02 1.14e+00
  ... (remaining 8926 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 11542
        1.56 -     3.11: 440
        3.11 -     4.67: 71
        4.67 -     6.22: 21
        6.22 -     7.78: 5
  Bond angle restraints: 12079
  Sorted by residual:
  angle pdb=" N   ILE B  33 "
        pdb=" CA  ILE B  33 "
        pdb=" C   ILE B  33 "
      ideal   model   delta    sigma   weight residual
     113.39  108.56    4.83 1.47e+00 4.63e-01 1.08e+01
  angle pdb=" N   SER B 331 "
        pdb=" CA  SER B 331 "
        pdb=" C   SER B 331 "
      ideal   model   delta    sigma   weight residual
     108.34  112.57   -4.23 1.31e+00 5.83e-01 1.04e+01
  angle pdb=" C   LEU B 252 "
        pdb=" N   PHE B 253 "
        pdb=" CA  PHE B 253 "
      ideal   model   delta    sigma   weight residual
     122.87  128.07   -5.20 1.61e+00 3.86e-01 1.04e+01
  angle pdb=" N   SER A  13 "
        pdb=" CA  SER A  13 "
        pdb=" C   SER A  13 "
      ideal   model   delta    sigma   weight residual
     108.13  113.63   -5.50 1.72e+00 3.38e-01 1.02e+01
  angle pdb=" CA  CYS E 147 "
        pdb=" CB  CYS E 147 "
        pdb=" SG  CYS E 147 "
      ideal   model   delta    sigma   weight residual
     114.40  121.55   -7.15 2.30e+00 1.89e-01 9.67e+00
  ... (remaining 12074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 4825
       17.53 -    35.06: 398
       35.06 -    52.60: 59
       52.60 -    70.13: 5
       70.13 -    87.66: 3
  Dihedral angle restraints: 5290
    sinusoidal: 2086
      harmonic: 3204
  Sorted by residual:
  dihedral pdb=" CA  GLY B 202 "
           pdb=" C   GLY B 202 "
           pdb=" N   ALA B 203 "
           pdb=" CA  ALA B 203 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.49  -25.51     0      5.00e+00 4.00e-02 2.60e+01
  dihedral pdb=" CB  CYS E 147 "
           pdb=" SG  CYS E 147 "
           pdb=" SG  CYS E 217 "
           pdb=" CB  CYS E 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  130.87  -37.87     1      1.00e+01 1.00e-02 2.02e+01
  dihedral pdb=" CA  ALA B 203 "
           pdb=" C   ALA B 203 "
           pdb=" N   CYS B 204 "
           pdb=" CA  CYS B 204 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.79   22.21     0      5.00e+00 4.00e-02 1.97e+01
  ... (remaining 5287 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 692
       0.029 -    0.058: 404
       0.058 -    0.088: 167
       0.088 -    0.117: 84
       0.117 -    0.146: 26
  Chirality restraints: 1373
  Sorted by residual:
  chirality pdb=" CA  ASN B 237 "
            pdb=" N   ASN B 237 "
            pdb=" C   ASN B 237 "
            pdb=" CB  ASN B 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.32e-01
  chirality pdb=" CA  ILE A  43 "
            pdb=" N   ILE A  43 "
            pdb=" C   ILE A  43 "
            pdb=" CB  ILE A  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.92e-01
  chirality pdb=" CA  PRO G  49 "
            pdb=" N   PRO G  49 "
            pdb=" C   PRO G  49 "
            pdb=" CB  PRO G  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.92e-01
  ... (remaining 1370 not shown)

  Planarity restraints: 1519
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG R 680 "    0.035 5.00e-02 4.00e+02   5.29e-02 4.47e+00
        pdb=" N   PRO R 681 "   -0.091 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=" CA  VAL R 712 "    0.009 2.00e-02 2.50e+03   1.82e-02 3.30e+00
        pdb=" C   VAL R 712 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   VAL R 712 "    0.012 2.00e-02 2.50e+03
        pdb=" N   THR R 713 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 726 "   -0.030 5.00e-02 4.00e+02   4.49e-02 3.23e+00
        pdb=" N   PRO R 727 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO R 727 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO R 727 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1516 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 501
        2.73 -     3.27: 8190
        3.27 -     3.81: 12943
        3.81 -     4.36: 15016
        4.36 -     4.90: 26925
  Nonbonded interactions: 63575
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 298 "
            pdb=" NZ  LYS B 301 "
     model   vdw
     2.184 3.120
  nonbonded pdb=" N   SER R 531 "
            pdb=" OH  TYR R 683 "
     model   vdw
     2.262 3.120
  nonbonded pdb=" O   ASN B 340 "
            pdb=" NH2 ARG G  62 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" O   ASP B 333 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" NH2 ARG B 137 "
            pdb=" O   GLU B 172 "
     model   vdw
     2.297 3.120
  ... (remaining 63570 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.610
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7142
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      :  0.006   0.053   8931  Z= 0.396
  Angle     :  0.732   7.780  12079  Z= 0.417
  Chirality :  0.047   0.146   1373
  Planarity :  0.005   0.053   1519
  Dihedral  : 12.733  87.660   3216
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.31 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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 (0.25), residues: 1093
  helix:  1.01 (0.28), residues: 362
  sheet: -0.05 (0.32), residues: 272
  loop : -1.89 (0.27), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 169 
 HIS   0.010   0.002   HIS E 220 
 PHE   0.024   0.003   PHE R 627 
 TYR   0.021   0.002   TYR E 178 
 ARG   0.003   0.000   ARG E  72 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 166
  time to evaluate  : 1.019 
Fit side-chains
REVERT: A  262 ASP cc_start: 0.6499 (m-30) cc_final: 0.6256 (m-30)
REVERT: B  205 ASP cc_start: 0.7186 (t0) cc_final: 0.6881 (t0)
REVERT: B  291 ASP cc_start: 0.6365 (m-30) cc_final: 0.5908 (m-30)
REVERT: E  211 ASP cc_start: 0.7345 (m-30) cc_final: 0.7143 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 167
  average time/residue: 0.3088
  time to fit residues: 65.3630
Evaluate side-chains
  154 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 85 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0770
   chunk 63 optimal weight:    0.9990
   chunk 98 optimal weight:    0.0980
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
A 358 GLN
E 159 ASN
G  18 GLN
G  24 ASN
R 620 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
moved from start:          0.1139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8931  Z= 0.187
  Angle     :  0.563   7.385  12079  Z= 0.306
  Chirality :  0.042   0.155   1373
  Planarity :  0.004   0.050   1519
  Dihedral  :  4.757  20.796   1202
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  6.37 %
    Favored  : 92.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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: -0.00 (0.26), residues: 1093
  helix:  1.94 (0.28), residues: 365
  sheet:  0.16 (0.32), residues: 280
  loop : -1.83 (0.27), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.026   0.002   PHE A 273 
 TYR   0.014   0.001   TYR B 105 
 ARG   0.002   0.000   ARG E 179 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 174
  time to evaluate  : 0.797 
Fit side-chains
REVERT: A   33 GLU cc_start: 0.6982 (tt0) cc_final: 0.6738 (tt0)
REVERT: A  212 PHE cc_start: 0.7980 (p90) cc_final: 0.7576 (p90)
REVERT: A  262 ASP cc_start: 0.6416 (m-30) cc_final: 0.6171 (m-30)
REVERT: B   61 MET cc_start: 0.8276 (ppp) cc_final: 0.7918 (ppp)
REVERT: R  721 LYS cc_start: 0.7446 (mmtt) cc_final: 0.7239 (mmmm)
REVERT: R  761 ASP cc_start: 0.5414 (m-30) cc_final: 0.5108 (t70)
  outliers start: 10
  outliers final: 7
  residues processed: 177
  average time/residue: 0.3009
  time to fit residues: 67.2505
Evaluate side-chains
  166 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 159
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain R residue  695 SER
Chi-restraints excluded: chain R residue  705 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 30 optimal weight:    0.3980
   chunk 82 optimal weight:    0.0670
   chunk 67 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 99 optimal weight:    0.2980
   chunk 107 optimal weight:    0.6980
   chunk 88 optimal weight:    0.6980
   chunk 98 optimal weight:    0.0980
   chunk 33 optimal weight:    0.1980
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.2118

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

Flipped N/Q/H residues before XYZ refinement:
A 358 GLN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.1748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8931  Z= 0.133
  Angle     :  0.505   8.157  12079  Z= 0.269
  Chirality :  0.041   0.141   1373
  Planarity :  0.003   0.048   1519
  Dihedral  :  4.296  19.596   1202
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  9.30 %
    Favored  : 89.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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: 1093
  helix:  2.44 (0.28), residues: 367
  sheet:  0.38 (0.32), residues: 271
  loop : -1.75 (0.27), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.018   0.001   PHE A 273 
 TYR   0.008   0.001   TYR R 674 
 ARG   0.004   0.000   ARG B 251 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 165
  time to evaluate  : 1.000 
Fit side-chains
REVERT: A  212 PHE cc_start: 0.7963 (p90) cc_final: 0.7608 (p90)
REVERT: A  262 ASP cc_start: 0.6302 (m-30) cc_final: 0.6050 (m-30)
REVERT: B   61 MET cc_start: 0.8234 (ppp) cc_final: 0.7795 (ppp)
REVERT: B  332 TRP cc_start: 0.8371 (m-10) cc_final: 0.8122 (m-10)
REVERT: E  163 TYR cc_start: 0.7450 (m-80) cc_final: 0.7236 (m-80)
REVERT: R  721 LYS cc_start: 0.7318 (mmtt) cc_final: 0.7113 (mmtt)
  outliers start: 11
  outliers final: 5
  residues processed: 171
  average time/residue: 0.2925
  time to fit residues: 63.9328
Evaluate side-chains
  166 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 161
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain R residue  695 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    0.6980
   chunk 74 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0980
   chunk 10 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0570
   chunk 66 optimal weight:    0.9990
   chunk 99 optimal weight:    0.6980
   chunk 105 optimal weight:    0.9980
   chunk 94 optimal weight:    0.5980
   chunk 28 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.4098

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

Flipped N/Q/H residues before XYZ refinement:
A 358 GLN
B  75 GLN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8931  Z= 0.170
  Angle     :  0.522   7.634  12079  Z= 0.276
  Chirality :  0.041   0.137   1373
  Planarity :  0.003   0.048   1519
  Dihedral  :  4.231  19.700   1202
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 10.97 %
    Favored  : 87.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.51 (0.26), residues: 1093
  helix:  2.61 (0.28), residues: 365
  sheet:  0.36 (0.32), residues: 268
  loop : -1.66 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS E 220 
 PHE   0.014   0.001   PHE B 199 
 TYR   0.010   0.001   TYR E 178 
 ARG   0.003   0.000   ARG B 251 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 162
  time to evaluate  : 0.986 
Fit side-chains
REVERT: A  212 PHE cc_start: 0.7989 (p90) cc_final: 0.7606 (p90)
REVERT: A  252 ASP cc_start: 0.7194 (t70) cc_final: 0.6659 (m-30)
REVERT: A  262 ASP cc_start: 0.6314 (m-30) cc_final: 0.6061 (m-30)
REVERT: B   61 MET cc_start: 0.8313 (ppp) cc_final: 0.7756 (ppp)
REVERT: E  163 TYR cc_start: 0.7663 (m-80) cc_final: 0.7453 (m-80)
REVERT: R  687 ASP cc_start: 0.7876 (t0) cc_final: 0.7672 (m-30)
  outliers start: 12
  outliers final: 8
  residues processed: 165
  average time/residue: 0.2982
  time to fit residues: 62.6309
Evaluate side-chains
  164 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 156
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  354 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain R residue  695 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 59 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 78 optimal weight:    5.9990
   chunk 43 optimal weight:    0.0980
   chunk 89 optimal weight:    0.0670
   chunk 72 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 94 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.4718

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7070
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8931  Z= 0.180
  Angle     :  0.529   7.872  12079  Z= 0.280
  Chirality :  0.041   0.137   1373
  Planarity :  0.003   0.049   1519
  Dihedral  :  4.235  20.094   1202
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 11.91 %
    Favored  : 86.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.56 (0.26), residues: 1093
  helix:  2.64 (0.28), residues: 366
  sheet:  0.39 (0.32), residues: 268
  loop : -1.62 (0.27), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.004   0.001   HIS E 220 
 PHE   0.014   0.001   PHE B 199 
 TYR   0.011   0.001   TYR E 178 
 ARG   0.002   0.000   ARG B 251 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 156
  time to evaluate  : 0.990 
Fit side-chains
REVERT: A  212 PHE cc_start: 0.8014 (p90) cc_final: 0.7605 (p90)
REVERT: A  262 ASP cc_start: 0.6368 (m-30) cc_final: 0.6115 (m-30)
REVERT: B   19 ARG cc_start: 0.8126 (ttp-170) cc_final: 0.7674 (ttp-170)
REVERT: B   70 LEU cc_start: 0.7585 (mt) cc_final: 0.7248 (mt)
  outliers start: 13
  outliers final: 10
  residues processed: 162
  average time/residue: 0.2839
  time to fit residues: 59.5540
Evaluate side-chains
  165 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 155
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  354 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue  695 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 94 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 105 optimal weight:    0.3980
   chunk 87 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7112
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8931  Z= 0.259
  Angle     :  0.581   8.435  12079  Z= 0.307
  Chirality :  0.042   0.142   1373
  Planarity :  0.004   0.049   1519
  Dihedral  :  4.470  22.936   1202
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 12.85 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.46 (0.26), residues: 1093
  helix:  2.51 (0.28), residues: 367
  sheet:  0.45 (0.32), residues: 267
  loop : -1.72 (0.27), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 234 
 HIS   0.007   0.001   HIS E 220 
 PHE   0.015   0.002   PHE B 199 
 TYR   0.013   0.002   TYR E 178 
 ARG   0.003   0.000   ARG R 680 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 158
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
REVERT: A  212 PHE cc_start: 0.8085 (p90) cc_final: 0.7650 (p90)
REVERT: A  262 ASP cc_start: 0.6395 (m-30) cc_final: 0.6165 (m-30)
REVERT: B   19 ARG cc_start: 0.8134 (ttp-170) cc_final: 0.7708 (ttp-170)
REVERT: B  219 ARG cc_start: 0.7703 (ttm-80) cc_final: 0.7222 (mtt90)
REVERT: R  687 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7520 (m-30)
  outliers start: 17
  outliers final: 11
  residues processed: 166
  average time/residue: 0.2861
  time to fit residues: 61.0484
Evaluate side-chains
  166 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 154
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  354 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain E residue  117 LEU
Chi-restraints excluded: chain R residue  687 ASP
Chi-restraints excluded: chain R residue  695 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 77 optimal weight:    8.9990
   chunk 59 optimal weight:    0.9990
   chunk 88 optimal weight:    0.5980
   chunk 58 optimal weight:    0.6980
   chunk 105 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 358 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7110
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8931  Z= 0.253
  Angle     :  0.581   9.335  12079  Z= 0.307
  Chirality :  0.042   0.142   1373
  Planarity :  0.004   0.047   1519
  Dihedral  :  4.512  22.050   1202
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 14.52 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.43 (0.26), residues: 1093
  helix:  2.49 (0.28), residues: 366
  sheet:  0.43 (0.32), residues: 267
  loop : -1.74 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  82 
 HIS   0.006   0.001   HIS E 220 
 PHE   0.030   0.002   PHE A 273 
 TYR   0.012   0.002   TYR E 178 
 ARG   0.003   0.000   ARG R 680 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 154
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
REVERT: A  212 PHE cc_start: 0.8084 (p90) cc_final: 0.7665 (p90)
REVERT: A  262 ASP cc_start: 0.6370 (m-30) cc_final: 0.6147 (m-30)
REVERT: B   19 ARG cc_start: 0.8132 (ttp-170) cc_final: 0.7706 (ttp-170)
REVERT: B  219 ARG cc_start: 0.7625 (ttm-80) cc_final: 0.7133 (mtt90)
REVERT: R  687 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7461 (m-30)
  outliers start: 13
  outliers final: 11
  residues processed: 161
  average time/residue: 0.2979
  time to fit residues: 61.0720
Evaluate side-chains
  167 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 155
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain A residue  354 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain E residue  117 LEU
Chi-restraints excluded: chain R residue  678 TYR
Chi-restraints excluded: chain R residue  687 ASP
Chi-restraints excluded: chain R residue  695 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0030
   chunk 20 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0970
   chunk 82 optimal weight:    1.9990
   chunk 95 optimal weight:    0.4980
   chunk 100 optimal weight:    0.6980
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.4188

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

Flipped N/Q/H residues before XYZ refinement:
A 358 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7072
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8931  Z= 0.173
  Angle     :  0.550   9.164  12079  Z= 0.287
  Chirality :  0.041   0.138   1373
  Planarity :  0.003   0.049   1519
  Dihedral  :  4.281  19.823   1202
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 14.63 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.58 (0.26), residues: 1093
  helix:  2.66 (0.28), residues: 367
  sheet:  0.45 (0.32), residues: 267
  loop : -1.66 (0.27), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.026   0.001   PHE A 273 
 TYR   0.009   0.001   TYR E 102 
 ARG   0.003   0.000   ARG E 148 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 157
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
REVERT: A  212 PHE cc_start: 0.8041 (p90) cc_final: 0.7619 (p90)
REVERT: A  262 ASP cc_start: 0.6345 (m-30) cc_final: 0.6114 (m-30)
REVERT: B   19 ARG cc_start: 0.8130 (ttp-170) cc_final: 0.7705 (ttp-170)
REVERT: R  687 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7485 (m-30)
  outliers start: 14
  outliers final: 10
  residues processed: 166
  average time/residue: 0.2985
  time to fit residues: 63.4389
Evaluate side-chains
  167 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 156
  time to evaluate  : 1.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain E residue  117 LEU
Chi-restraints excluded: chain R residue  678 TYR
Chi-restraints excluded: chain R residue  687 ASP
Chi-restraints excluded: chain R residue  695 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    0.0020
   chunk 100 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9990
   chunk 30 optimal weight:    0.4980
   chunk 88 optimal weight:    0.7980
   chunk 92 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9990
   chunk 103 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 358 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8931  Z= 0.201
  Angle     :  0.579   9.463  12079  Z= 0.301
  Chirality :  0.041   0.143   1373
  Planarity :  0.003   0.049   1519
  Dihedral  :  4.331  21.294   1202
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 14.63 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.64 (0.26), residues: 1093
  helix:  2.76 (0.27), residues: 362
  sheet:  0.49 (0.32), residues: 267
  loop : -1.62 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.006   0.001   HIS E 220 
 PHE   0.024   0.002   PHE A 273 
 TYR   0.010   0.001   TYR E 102 
 ARG   0.003   0.000   ARG E 179 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 157
  time to evaluate  : 1.442 
Fit side-chains
REVERT: A  212 PHE cc_start: 0.8056 (p90) cc_final: 0.7643 (p90)
REVERT: A  262 ASP cc_start: 0.6356 (m-30) cc_final: 0.6122 (m-30)
REVERT: B   19 ARG cc_start: 0.8130 (ttp-170) cc_final: 0.7702 (ttp-170)
REVERT: E  164 TRP cc_start: 0.8351 (m100) cc_final: 0.7693 (m100)
REVERT: R  687 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7502 (m-30)
  outliers start: 17
  outliers final: 12
  residues processed: 166
  average time/residue: 0.3014
  time to fit residues: 63.9439
Evaluate side-chains
  170 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 157
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASP
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  284 MET
Chi-restraints excluded: chain A residue  354 ASP
Chi-restraints excluded: chain A residue  362 LYS
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain E residue  117 LEU
Chi-restraints excluded: chain R residue  687 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 108 optimal weight:    4.9990
   chunk 99 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 66 optimal weight:    0.5980
   chunk 53 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 92 optimal weight:    0.0570
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.7098

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

Flipped N/Q/H residues before XYZ refinement:
A 358 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7104
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8931  Z= 0.242
  Angle     :  0.606  10.095  12079  Z= 0.315
  Chirality :  0.042   0.143   1373
  Planarity :  0.004   0.049   1519
  Dihedral  :  4.428  21.997   1202
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 15.15 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.50 (0.26), residues: 1093
  helix:  2.55 (0.28), residues: 368
  sheet:  0.47 (0.32), residues: 268
  loop : -1.73 (0.27), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.006   0.001   HIS E 220 
 PHE   0.051   0.002   PHE E 227 
 TYR   0.012   0.002   TYR R 678 
 ARG   0.002   0.000   ARG E 148 

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 157
  time to evaluate  : 1.039 
Fit side-chains
REVERT: A  212 PHE cc_start: 0.8077 (p90) cc_final: 0.7646 (p90)
REVERT: A  262 ASP cc_start: 0.6372 (m-30) cc_final: 0.6142 (m-30)
REVERT: B   19 ARG cc_start: 0.8129 (ttp-170) cc_final: 0.7703 (ttp-170)
REVERT: B  205 ASP cc_start: 0.7173 (t0) cc_final: 0.6909 (t0)
REVERT: B  219 ARG cc_start: 0.7610 (ttm-80) cc_final: 0.7119 (mtt90)
  outliers start: 12
  outliers final: 11
  residues processed: 164
  average time/residue: 0.3139
  time to fit residues: 65.2404
Evaluate side-chains
  165 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 154
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASP
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  362 LYS
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain E residue  117 LEU
Chi-restraints excluded: chain R residue  695 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 36 optimal weight:    0.2980
   chunk 88 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0270
   chunk 76 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.5238

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

Flipped N/Q/H residues before XYZ refinement:
A 358 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.147898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.121604 restraints weight = 12744.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 2.60
r_work: 0.3470 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8931  Z= 0.197
  Angle     :  0.590  10.483  12079  Z= 0.303
  Chirality :  0.041   0.140   1373
  Planarity :  0.004   0.049   1519
  Dihedral  :  4.326  20.816   1202
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 15.46 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  0.55 (0.26), residues: 1093
  helix:  2.62 (0.28), residues: 368
  sheet:  0.51 (0.32), residues: 267
  loop : -1.71 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.004   0.001   HIS E 220 
 PHE   0.042   0.002   PHE E 227 
 TYR   0.009   0.001   TYR E 102 
 ARG   0.006   0.000   ARG E 148 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2272.65 seconds
wall clock time: 42 minutes 3.35 seconds (2523.35 seconds total)