Starting phenix.real_space_refine
on Mon May 12 05:55:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e9z_27969/05_2025/8e9z_27969.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e9z_27969/05_2025/8e9z_27969.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8e9z_27969/05_2025/8e9z_27969.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e9z_27969/05_2025/8e9z_27969.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e9z_27969/05_2025/8e9z_27969.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e9z_27969/05_2025/8e9z_27969.cif"
  }
  resolution = 2.69
  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      54      5.16       5
     C    5488      2.51       5
     N    1443      2.21       5
     O    1581      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8566
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2173
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2173
          Classifications: {'peptide': 278}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 9, 'TRANS': 268}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 73
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 68
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 26
    Chain: "B"
      Number of atoms: 1698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1698
          Classifications: {'peptide': 222}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 6, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 116
          Unresolved non-hydrogen angles: 138
          Unresolved non-hydrogen dihedrals: 96
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 6, 'PHE:plan': 1, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 83
    Chain: "C"
      Number of atoms: 2504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2504
          Classifications: {'peptide': 339}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 102
          Unresolved non-hydrogen angles: 124
          Unresolved non-hydrogen dihedrals: 80
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 6, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 72
    Chain: "D"
      Number of atoms: 397
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 397
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 33
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "E"
      Number of atoms: 1745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1745
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 33
    Chain: "A"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 49
          Unusual residues: {'IXO': 1, 'Y01': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.97, per 1000 atoms: 0.58
  Number of scatterers: 8566
  At special positions: 0
  Unit cell: (88, 120.56, 124.96, 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      54     16.00
     O    1581      8.00
     N    1443      7.00
     C    5488      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 141 " - pdb=" SG  CYS A 221 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 517 " - pdb=" SG  CYS A 520 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " 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: 1.94
  Conformation dependent library (CDL) restraints added in 960.2 milliseconds
  

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2118

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 12 sheets defined
      35.9% alpha, 21.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 68 through 96
      removed outlier: 3.866A  pdb=" N   ALA A  72 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   THR A  82 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   VAL A  89 " --> pdb=" O   GLY A  85 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ILE A  90 " --> pdb=" O   ASN A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 100
    Processing helix  chain 'A' and resid 104 through 120
      removed outlier: 3.615A  pdb=" N   ILE A 116 " --> pdb=" O   CYS A 112 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ILE A 117 " --> pdb=" O   ALA A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.815A  pdb=" N   THR A 127 " --> pdb=" O   ASN A 123 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   TYR A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 172
      removed outlier: 4.089A  pdb=" N   ASP A 142 " --> pdb=" O   ASN A 138 " (cutoff:3.500A)
      removed outlier: 5.422A  pdb=" N   LEU A 143 " --> pdb=" O   LEU A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 206
      removed outlier: 3.830A  pdb=" N   VAL A 187 " --> pdb=" O   LYS A 183 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   MET A 188 " --> pdb=" O   ARG A 184 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   SER A 196 " --> pdb=" O   ALA A 192 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   TRP A 200 " --> pdb=" O   SER A 196 " (cutoff:3.500A)
      Proline residue:  A 202  - end of helix
    Processing helix  chain 'A' and resid 231 through 238
    Processing helix  chain 'A' and resid 240 through 265
    Processing helix  chain 'A' and resid 487 through 502
      removed outlier: 3.953A  pdb=" N   GLN A 491 " --> pdb=" O   LYS A 487 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   PHE A 500 " --> pdb=" O   ILE A 496 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ILE A 501 " --> pdb=" O   LEU A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 517
      removed outlier: 3.875A  pdb=" N   LEU A 512 " --> pdb=" O   ASN A 508 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   VAL A 513 " --> pdb=" O   ILE A 509 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ASN A 514 " --> pdb=" O   MET A 510 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   THR A 515 " --> pdb=" O   VAL A 511 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   PHE A 516 " --> pdb=" O   LEU A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 532
      removed outlier: 3.544A  pdb=" N   LEU A 528 " --> pdb=" O   THR A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 544
      Proline residue:  A 541  - end of helix
    Processing helix  chain 'A' and resid 548 through 561
    Processing helix  chain 'B' and resid 6 through 31
      removed outlier: 3.961A  pdb=" N   ASP B  26 " --> pdb=" O   ASN B  22 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLY B  27 " --> pdb=" O   LEU B  23 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LYS B  29 " --> pdb=" O   GLU B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 49
      removed outlier: 3.744A  pdb=" N   ILE B  49 " --> pdb=" O   LYS B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 102
      removed outlier: 3.604A  pdb=" N   ILE B  97 " --> pdb=" O   ARG B  94 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLN B  98 " --> pdb=" O   LYS B  95 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ASN B 101 " --> pdb=" O   GLN B  98 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   ASP B 102 " --> pdb=" O   CYS B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 130
    Processing helix  chain 'B' and resid 147 through 155
      removed outlier: 3.743A  pdb=" N   GLU B 151 " --> pdb=" O   ASP B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 164
      removed outlier: 4.159A  pdb=" N   TYR B 163 " --> pdb=" O   LYS B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 202
      removed outlier: 3.550A  pdb=" N   ILE B 193 " --> pdb=" O   ALA B 189 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   PHE B 197 " --> pdb=" O   ILE B 193 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   ILE B 200 " --> pdb=" O   GLU B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 242
      removed outlier: 3.573A  pdb=" N   GLU B 242 " --> pdb=" O   MET B 238 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3 through 24
      removed outlier: 3.534A  pdb=" N   GLU C  10 " --> pdb=" O   GLN C   6 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'D' and resid 7 through 24
      removed outlier: 3.582A  pdb=" N   ASN D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 43
      removed outlier: 3.649A  pdb=" N   CYS D  41 " --> pdb=" O   LEU D  37 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 44 through 48
      removed outlier: 3.527A  pdb=" N   ASP D  48 " --> pdb=" O   ALA D  45 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.512A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 75
      removed outlier: 3.648A  pdb=" N   PHE B  74 " --> pdb=" O   PHE B  81 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   VAL B  86 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 7.380A  pdb=" N   GLY B  40 " --> pdb=" O   VAL B  86 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   ARG B  35 " --> pdb=" O   ALA B 105 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   ILE B 107 " --> pdb=" O   ARG B  35 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   LEU B  37 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 7.712A  pdb=" N   VAL B 109 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   LEU B  39 " --> pdb=" O   VAL B 109 " (cutoff:3.500A)
      removed outlier: 8.636A  pdb=" N   ASP B 111 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   ILE B 106 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 7.446A  pdb=" N   PHE B 142 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   PHE B 108 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   ASN B 144 " --> pdb=" O   PHE B 108 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   VAL B 110 " --> pdb=" O   ASN B 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51
      removed outlier: 3.718A  pdb=" N   ARG C  49 " --> pdb=" O   ILE C 338 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   GLY C 330 " --> pdb=" O   CYS C 317 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   CYS C 317 " --> pdb=" O   GLY C 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63
      removed outlier: 3.683A  pdb=" N   SER C  74 " --> pdb=" O   LYS C  78 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   ASP C  83 " --> pdb=" O   LYS C  89 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   LYS C  89 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.891A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 5.055A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.328A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   CYS C 121 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   GLU C 138 " --> pdb=" O   CYS C 121 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ILE C 123 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151
      removed outlier: 3.544A  pdb=" N   CYS C 148 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192
      removed outlier: 3.554A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.260A  pdb=" N   ASP C 254 " --> pdb=" O   GLU C 260 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   GLU C 260 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.521A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   CYS C 294 " --> pdb=" O   VAL C 307 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   VAL C 307 " --> pdb=" O   CYS C 294 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   VAL C 296 " --> pdb=" O   ALA C 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.886A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   THR E 115 " --> pdb=" O   TYR E  94 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 136
      removed outlier: 6.632A  pdb=" N   LEU E 162 " --> pdb=" O   TYR E 178 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   TYR E 178 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 143 through 148

    400 hydrogen bonds defined for protein.
    1128 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: 2.22

  Time building geometry restraints manager: 2.30 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1374
        1.31 -     1.43: 2450
        1.43 -     1.56: 4851
        1.56 -     1.68: 3
        1.68 -     1.81: 76
  Bond restraints: 8754
  Sorted by residual:
  bond pdb=" C   TYR E 178 "
       pdb=" N   ARG E 179 "
    ideal  model  delta    sigma   weight residual
    1.333  1.419 -0.086 1.39e-02 5.18e+03 3.85e+01
  bond pdb=" N   PRO B 173 "
       pdb=" CA  PRO B 173 "
    ideal  model  delta    sigma   weight residual
    1.467  1.424  0.043 1.21e-02 6.83e+03 1.27e+01
  bond pdb=" C   ARG E 179 "
       pdb=" N   MET E 180 "
    ideal  model  delta    sigma   weight residual
    1.332  1.289  0.043 1.40e-02 5.10e+03 9.62e+00
  bond pdb=" C   TYR E  95 "
       pdb=" N   CYS E  96 "
    ideal  model  delta    sigma   weight residual
    1.330  1.368 -0.038 1.32e-02 5.74e+03 8.27e+00
  bond pdb=" N   PHE B 167 "
       pdb=" CA  PHE B 167 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.19e-02 7.06e+03 8.20e+00
  ... (remaining 8749 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 11570
        2.03 -     4.05: 285
        4.05 -     6.08: 56
        6.08 -     8.11: 17
        8.11 -    10.13: 6
  Bond angle restraints: 11934
  Sorted by residual:
  angle pdb=" CA  TYR E 223 "
        pdb=" C   TYR E 223 "
        pdb=" O   TYR E 223 "
      ideal   model   delta    sigma   weight residual
     120.25  110.12   10.13 1.08e+00 8.57e-01 8.80e+01
  angle pdb=" CA  TYR E 223 "
        pdb=" C   TYR E 223 "
        pdb=" N   PRO E 224 "
      ideal   model   delta    sigma   weight residual
     118.23  125.10   -6.87 9.20e-01 1.18e+00 5.57e+01
  angle pdb=" N   ASP B 175 "
        pdb=" CA  ASP B 175 "
        pdb=" C   ASP B 175 "
      ideal   model   delta    sigma   weight residual
     111.28  103.98    7.30 1.09e+00 8.42e-01 4.48e+01
  angle pdb=" N   PRO B 173 "
        pdb=" CA  PRO B 173 "
        pdb=" C   PRO B 173 "
      ideal   model   delta    sigma   weight residual
     111.14  101.09   10.05 1.56e+00 4.11e-01 4.15e+01
  angle pdb=" N   ALA B 176 "
        pdb=" CA  ALA B 176 "
        pdb=" C   ALA B 176 "
      ideal   model   delta    sigma   weight residual
     109.23   99.98    9.25 1.55e+00 4.16e-01 3.56e+01
  ... (remaining 11929 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.93: 4937
       28.93 -    57.86: 212
       57.86 -    86.79: 21
       86.79 -   115.72: 0
      115.72 -   144.65: 1
  Dihedral angle restraints: 5171
    sinusoidal: 1891
      harmonic: 3280
  Sorted by residual:
  dihedral pdb=" CB  CYS A 517 "
           pdb=" SG  CYS A 517 "
           pdb=" SG  CYS A 520 "
           pdb=" CB  CYS A 520 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -147.99   61.99     1      1.00e+01 1.00e-02 5.09e+01
  dihedral pdb=" C   CYS C 233 "
           pdb=" N   CYS C 233 "
           pdb=" CA  CYS C 233 "
           pdb=" CB  CYS C 233 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.46  -11.14     0      2.50e+00 1.60e-01 1.98e+01
  dihedral pdb=" C05 IXO A 801 "
           pdb=" C06 IXO A 801 "
           pdb=" C07 IXO A 801 "
           pdb=" C08 IXO A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     181.37   36.72  144.65     1      3.00e+01 1.11e-03 1.94e+01
  ... (remaining 5168 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1189
       0.066 -    0.132: 177
       0.132 -    0.199: 14
       0.199 -    0.265: 9
       0.265 -    0.331: 3
  Chirality restraints: 1392
  Sorted by residual:
  chirality pdb=" CBG Y01 A 802 "
            pdb=" CAQ Y01 A 802 "
            pdb=" CBD Y01 A 802 "
            pdb=" CBI Y01 A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.66    0.33 2.00e-01 2.50e+01 2.74e+00
  chirality pdb=" CBF Y01 A 802 "
            pdb=" CAS Y01 A 802 "
            pdb=" CBD Y01 A 802 "
            pdb=" CBH Y01 A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.77    0.32 2.00e-01 2.50e+01 2.57e+00
  chirality pdb=" CA  ARG B 169 "
            pdb=" N   ARG B 169 "
            pdb=" C   ARG B 169 "
            pdb=" CB  ARG B 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.82   -0.31 2.00e-01 2.50e+01 2.37e+00
  ... (remaining 1389 not shown)

  Planarity restraints: 1500
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR E 223 "   -0.021 2.00e-02 2.50e+03   4.16e-02 1.73e+01
        pdb=" C   TYR E 223 "    0.072 2.00e-02 2.50e+03
        pdb=" O   TYR E 223 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   PRO E 224 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 165 "    0.018 2.00e-02 2.50e+03   3.62e-02 1.31e+01
        pdb=" C   PRO B 165 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   PRO B 165 "    0.024 2.00e-02 2.50e+03
        pdb=" N   GLU B 166 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 131 "   -0.016 2.00e-02 2.50e+03   3.21e-02 1.03e+01
        pdb=" C   MET A 131 "    0.055 2.00e-02 2.50e+03
        pdb=" O   MET A 131 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ASN A 132 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1497 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1861
        2.78 -     3.31: 7462
        3.31 -     3.84: 14339
        3.84 -     4.37: 16774
        4.37 -     4.90: 29326
  Nonbonded interactions: 69762
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B   8 "
            pdb=" OH  TYR E 163 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   ILE C  58 "
            pdb=" OG  SER C 316 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OG1 THR C 128 "
            pdb=" O   ARG C 129 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OD1 ASP E 211 "
            pdb=" OH  TYR E 215 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   GLN C  75 "
            pdb=" OG  SER C  98 "
     model   vdw
     2.313 3.040
  ... (remaining 69757 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:             1.650
  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:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.450
  Find NCS groups from input model:        0.080
  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:             0.000
  Load rotamer database and sin/cos tables:9.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
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      :  0.004   0.086   8757  Z= 0.249
  Angle     :  0.799  10.132  11940  Z= 0.488
  Chirality :  0.052   0.331   1392
  Planarity :  0.006   0.071   1500
  Dihedral  : 15.373 144.649   3044
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  : 14.56 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: -1.79 (0.23), residues: 1111
  helix: -2.53 (0.18), residues: 364
  sheet:  0.50 (0.31), residues: 286
  loop : -0.96 (0.27), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 531 
 HIS   0.009   0.002   HIS E  35 
 PHE   0.016   0.001   PHE C 234 
 TYR   0.034   0.002   TYR B 170 
 ARG   0.017   0.000   ARG C 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27231 (  400)
  hydrogen bonds       : angle       8.97325 ( 1128)
  SS BOND              : bond        0.00228 (    3)
  SS BOND              : angle       0.25368 (    6)
  covalent geometry    : bond        0.00407 ( 8754)
  covalent geometry    : angle       0.79954 (11934)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 168
  time to evaluate  : 0.904 
Fit side-chains
REVERT: C  283 ARG cc_start: 0.8430 (tpt-90) cc_final: 0.8079 (tpt90)
REVERT: E   68 PHE cc_start: 0.8234 (m-10) cc_final: 0.7832 (m-10)
REVERT: E  211 ASP cc_start: 0.7398 (t0) cc_final: 0.7043 (t0)
  outliers start: 3
  outliers final: 0
  residues processed: 169
  average time/residue: 0.9568
  time to fit residues: 174.9480
Evaluate side-chains
  163 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 99 optimal weight:    0.0270
   overall best weight:    0.8640

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

Flipped N/Q/H residues before XYZ refinement:
A 514 ASN
A 536 ASN
C 230 ASN
C 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.140534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.121948 restraints weight = 11853.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 1.82
r_work: 0.3474 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.1386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8757  Z= 0.198
  Angle     :  0.581   6.135  11940  Z= 0.314
  Chirality :  0.044   0.179   1392
  Planarity :  0.005   0.049   1500
  Dihedral  :  6.696  58.975   1293
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.14 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: -0.17 (0.25), residues: 1111
  helix:  0.15 (0.26), residues: 368
  sheet:  0.42 (0.30), residues: 298
  loop : -0.55 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 169 
 HIS   0.005   0.001   HIS B 209 
 PHE   0.022   0.002   PHE A 225 
 TYR   0.015   0.002   TYR A 128 
 ARG   0.004   0.001   ARG C 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05277 (  400)
  hydrogen bonds       : angle       5.25218 ( 1128)
  SS BOND              : bond        0.00607 (    3)
  SS BOND              : angle       1.07477 (    6)
  covalent geometry    : bond        0.00453 ( 8754)
  covalent geometry    : angle       0.58044 (11934)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 186
  time to evaluate  : 0.965 
Fit side-chains
REVERT: A  493 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7763 (mt)
REVERT: B  220 ASP cc_start: 0.7612 (t0) cc_final: 0.7409 (t0)
REVERT: E   68 PHE cc_start: 0.8241 (m-10) cc_final: 0.7938 (m-10)
  outliers start: 23
  outliers final: 7
  residues processed: 196
  average time/residue: 0.9266
  time to fit residues: 196.8797
Evaluate side-chains
  189 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 181
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  277 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   63 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 106 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0170
   chunk 56 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    0.7220

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

Flipped N/Q/H residues before XYZ refinement:
A 514 ASN
A 536 ASN
B 123 ASN
C 230 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.140448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.121864 restraints weight = 11945.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 1.83
r_work: 0.3479 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.1554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8757  Z= 0.171
  Angle     :  0.554   7.995  11940  Z= 0.296
  Chirality :  0.043   0.184   1392
  Planarity :  0.004   0.044   1500
  Dihedral  :  6.577  58.459   1293
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 15.83 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.30 (0.26), residues: 1111
  helix:  0.93 (0.28), residues: 367
  sheet:  0.36 (0.30), residues: 299
  loop : -0.42 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 169 
 HIS   0.006   0.001   HIS B  82 
 PHE   0.020   0.002   PHE A 225 
 TYR   0.012   0.001   TYR A 128 
 ARG   0.005   0.000   ARG C 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04592 (  400)
  hydrogen bonds       : angle       4.96262 ( 1128)
  SS BOND              : bond        0.00527 (    3)
  SS BOND              : angle       0.82557 (    6)
  covalent geometry    : bond        0.00388 ( 8754)
  covalent geometry    : angle       0.55394 (11934)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 182
  time to evaluate  : 0.856 
Fit side-chains
REVERT: A  493 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7730 (mt)
REVERT: E   68 PHE cc_start: 0.8239 (m-10) cc_final: 0.7937 (m-10)
  outliers start: 33
  outliers final: 17
  residues processed: 196
  average time/residue: 0.8730
  time to fit residues: 185.6080
Evaluate side-chains
  198 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 180
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  508 ASN
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain B residue   24 ARG
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  145 LYS
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  268 ASN
Chi-restraints excluded: chain C residue  277 SER
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   63 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 70 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0770
   chunk 28 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 105 optimal weight:    0.4980
   chunk 11 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A 514 ASN
A 536 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.139928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.122171 restraints weight = 12119.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 1.78
r_work: 0.3477 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.1661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8757  Z= 0.148
  Angle     :  0.540   6.650  11940  Z= 0.289
  Chirality :  0.042   0.178   1392
  Planarity :  0.004   0.043   1500
  Dihedral  :  6.509  59.284   1293
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 17.89 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.48 (0.26), residues: 1111
  helix:  1.23 (0.28), residues: 367
  sheet:  0.37 (0.30), residues: 300
  loop : -0.38 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 169 
 HIS   0.010   0.001   HIS B  82 
 PHE   0.019   0.002   PHE A 225 
 TYR   0.012   0.001   TYR A 507 
 ARG   0.007   0.000   ARG C 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04239 (  400)
  hydrogen bonds       : angle       4.83952 ( 1128)
  SS BOND              : bond        0.00461 (    3)
  SS BOND              : angle       0.71598 (    6)
  covalent geometry    : bond        0.00338 ( 8754)
  covalent geometry    : angle       0.54012 (11934)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 183
  time to evaluate  : 0.842 
Fit side-chains
REVERT: A  493 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7707 (mt)
REVERT: B  245 LEU cc_start: 0.7941 (mt) cc_final: 0.7689 (mp)
REVERT: E   68 PHE cc_start: 0.8224 (m-10) cc_final: 0.7976 (m-10)
  outliers start: 29
  outliers final: 19
  residues processed: 194
  average time/residue: 0.8612
  time to fit residues: 181.3799
Evaluate side-chains
  202 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 182
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 SER
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  508 ASN
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain B residue   24 ARG
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  145 LYS
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  268 ASN
Chi-restraints excluded: chain C residue  277 SER
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   63 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 54 optimal weight:    0.4980
   chunk 85 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0040
   chunk 83 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0770
   chunk 47 optimal weight:    0.6980
   chunk 104 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    0.4350

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

Flipped N/Q/H residues before XYZ refinement:
A 132 ASN
A 514 ASN
A 536 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.139929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.122092 restraints weight = 12060.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 1.79
r_work: 0.3477 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3335 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8757  Z= 0.148
  Angle     :  0.540   6.650  11940  Z= 0.289
  Chirality :  0.042   0.178   1392
  Planarity :  0.004   0.043   1500
  Dihedral  :  6.509  59.284   1293
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.50 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.48 (0.26), residues: 1111
  helix:  1.23 (0.28), residues: 367
  sheet:  0.37 (0.30), residues: 300
  loop : -0.38 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 169 
 HIS   0.010   0.001   HIS B  82 
 PHE   0.019   0.002   PHE A 225 
 TYR   0.012   0.001   TYR A 507 
 ARG   0.007   0.000   ARG C 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04239 (  400)
  hydrogen bonds       : angle       4.83952 ( 1128)
  SS BOND              : bond        0.00461 (    3)
  SS BOND              : angle       0.71598 (    6)
  covalent geometry    : bond        0.00338 ( 8754)
  covalent geometry    : angle       0.54012 (11934)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 181
  time to evaluate  : 0.840 
Fit side-chains
REVERT: A  493 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7704 (mt)
REVERT: B  245 LEU cc_start: 0.7956 (mt) cc_final: 0.7695 (mp)
REVERT: E   68 PHE cc_start: 0.8220 (m-10) cc_final: 0.7966 (m-10)
  outliers start: 20
  outliers final: 19
  residues processed: 189
  average time/residue: 0.8797
  time to fit residues: 179.9360
Evaluate side-chains
  200 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 SER
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  508 ASN
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain B residue   24 ARG
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  145 LYS
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  268 ASN
Chi-restraints excluded: chain C residue  277 SER
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   63 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 52 optimal weight:    0.1980
   chunk 80 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   chunk 95 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 102 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 97 optimal weight:    0.5980
   chunk 83 optimal weight:    1.9990
   chunk 96 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 536 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.139916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.122082 restraints weight = 12073.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 1.79
r_work: 0.3490 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3348 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8757  Z= 0.148
  Angle     :  0.540   6.650  11940  Z= 0.289
  Chirality :  0.042   0.178   1392
  Planarity :  0.004   0.043   1500
  Dihedral  :  6.509  59.284   1293
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.61 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.48 (0.26), residues: 1111
  helix:  1.23 (0.28), residues: 367
  sheet:  0.37 (0.30), residues: 300
  loop : -0.38 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 169 
 HIS   0.010   0.001   HIS B  82 
 PHE   0.019   0.002   PHE A 225 
 TYR   0.012   0.001   TYR A 507 
 ARG   0.007   0.000   ARG C 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04239 (  400)
  hydrogen bonds       : angle       4.83952 ( 1128)
  SS BOND              : bond        0.00461 (    3)
  SS BOND              : angle       0.71598 (    6)
  covalent geometry    : bond        0.00338 ( 8754)
  covalent geometry    : angle       0.54012 (11934)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 0.960 
Fit side-chains
REVERT: A  493 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7700 (mt)
REVERT: B  245 LEU cc_start: 0.7951 (mt) cc_final: 0.7692 (mp)
REVERT: E   68 PHE cc_start: 0.8222 (m-10) cc_final: 0.7968 (m-10)
  outliers start: 20
  outliers final: 19
  residues processed: 188
  average time/residue: 0.9036
  time to fit residues: 183.9443
Evaluate side-chains
  200 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 SER
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  508 ASN
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain B residue   24 ARG
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  145 LYS
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  268 ASN
Chi-restraints excluded: chain C residue  277 SER
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   63 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0570
   chunk 56 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0570
   chunk 67 optimal weight:    0.1980
   overall best weight:    0.3816

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

Flipped N/Q/H residues before XYZ refinement:
A 536 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.139908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.122133 restraints weight = 12143.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 1.78
r_work: 0.3493 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3352 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8757  Z= 0.148
  Angle     :  0.540   6.650  11940  Z= 0.289
  Chirality :  0.042   0.178   1392
  Planarity :  0.004   0.043   1500
  Dihedral  :  6.509  59.284   1293
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.61 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.48 (0.26), residues: 1111
  helix:  1.23 (0.28), residues: 367
  sheet:  0.37 (0.30), residues: 300
  loop : -0.38 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 169 
 HIS   0.010   0.001   HIS B  82 
 PHE   0.019   0.002   PHE A 225 
 TYR   0.012   0.001   TYR A 507 
 ARG   0.007   0.000   ARG C 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04239 (  400)
  hydrogen bonds       : angle       4.83952 ( 1128)
  SS BOND              : bond        0.00461 (    3)
  SS BOND              : angle       0.71598 (    6)
  covalent geometry    : bond        0.00338 ( 8754)
  covalent geometry    : angle       0.54012 (11934)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 0.864 
Fit side-chains
REVERT: A  493 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7701 (mt)
REVERT: B  245 LEU cc_start: 0.7949 (mt) cc_final: 0.7689 (mp)
REVERT: E   68 PHE cc_start: 0.8224 (m-10) cc_final: 0.7966 (m-10)
  outliers start: 20
  outliers final: 19
  residues processed: 188
  average time/residue: 0.9075
  time to fit residues: 185.1321
Evaluate side-chains
  200 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 SER
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  508 ASN
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain B residue   24 ARG
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  145 LYS
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  268 ASN
Chi-restraints excluded: chain C residue  277 SER
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   63 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 106 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9980
   chunk 91 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 64 optimal weight:    0.4980
   chunk 49 optimal weight:   10.0000
   chunk 94 optimal weight:    0.0050
   chunk 48 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
A 536 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.139908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.122035 restraints weight = 12376.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 1.81
r_work: 0.3474 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3332 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8757  Z= 0.148
  Angle     :  0.540   6.650  11940  Z= 0.289
  Chirality :  0.042   0.178   1392
  Planarity :  0.004   0.043   1500
  Dihedral  :  6.509  59.284   1293
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.61 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.48 (0.26), residues: 1111
  helix:  1.23 (0.28), residues: 367
  sheet:  0.37 (0.30), residues: 300
  loop : -0.38 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 169 
 HIS   0.010   0.001   HIS B  82 
 PHE   0.019   0.002   PHE A 225 
 TYR   0.012   0.001   TYR A 507 
 ARG   0.007   0.000   ARG C 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04239 (  400)
  hydrogen bonds       : angle       4.83952 ( 1128)
  SS BOND              : bond        0.00461 (    3)
  SS BOND              : angle       0.71598 (    6)
  covalent geometry    : bond        0.00338 ( 8754)
  covalent geometry    : angle       0.54012 (11934)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 0.853 
Fit side-chains
REVERT: A  493 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7703 (mt)
REVERT: B  245 LEU cc_start: 0.7958 (mt) cc_final: 0.7696 (mp)
REVERT: E   68 PHE cc_start: 0.8224 (m-10) cc_final: 0.7965 (m-10)
  outliers start: 20
  outliers final: 19
  residues processed: 188
  average time/residue: 0.8901
  time to fit residues: 181.4326
Evaluate side-chains
  200 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 SER
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  508 ASN
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain B residue   24 ARG
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  145 LYS
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  268 ASN
Chi-restraints excluded: chain C residue  277 SER
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   63 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 60 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0050
   chunk 102 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
A 536 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.139908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.122099 restraints weight = 12232.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 1.79
r_work: 0.3492 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3351 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8757  Z= 0.148
  Angle     :  0.540   6.650  11940  Z= 0.289
  Chirality :  0.042   0.178   1392
  Planarity :  0.004   0.043   1500
  Dihedral  :  6.509  59.284   1293
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.61 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.48 (0.26), residues: 1111
  helix:  1.23 (0.28), residues: 367
  sheet:  0.37 (0.30), residues: 300
  loop : -0.38 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 169 
 HIS   0.010   0.001   HIS B  82 
 PHE   0.019   0.002   PHE A 225 
 TYR   0.012   0.001   TYR A 507 
 ARG   0.007   0.000   ARG C 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04239 (  400)
  hydrogen bonds       : angle       4.83952 ( 1128)
  SS BOND              : bond        0.00461 (    3)
  SS BOND              : angle       0.71598 (    6)
  covalent geometry    : bond        0.00338 ( 8754)
  covalent geometry    : angle       0.54012 (11934)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 0.844 
Fit side-chains
REVERT: A  493 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7702 (mt)
REVERT: B  245 LEU cc_start: 0.7951 (mt) cc_final: 0.7690 (mp)
REVERT: E   68 PHE cc_start: 0.8223 (m-10) cc_final: 0.7966 (m-10)
  outliers start: 20
  outliers final: 19
  residues processed: 188
  average time/residue: 0.9254
  time to fit residues: 188.2867
Evaluate side-chains
  200 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 SER
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  508 ASN
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain B residue   24 ARG
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  145 LYS
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  268 ASN
Chi-restraints excluded: chain C residue  277 SER
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   63 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0870
   chunk 30 optimal weight:    0.5980
   chunk 15 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 91 optimal weight:    0.8980
   chunk 100 optimal weight:    0.0570
   chunk 53 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   chunk 96 optimal weight:    0.6980
   chunk 88 optimal weight:    0.0970
   overall best weight:    0.3074

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

Flipped N/Q/H residues before XYZ refinement:
A 536 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.139908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.122138 restraints weight = 12119.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 1.77
r_work: 0.3493 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3352 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8757  Z= 0.148
  Angle     :  0.540   6.650  11940  Z= 0.289
  Chirality :  0.042   0.178   1392
  Planarity :  0.004   0.043   1500
  Dihedral  :  6.509  59.284   1293
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.61 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.48 (0.26), residues: 1111
  helix:  1.23 (0.28), residues: 367
  sheet:  0.37 (0.30), residues: 300
  loop : -0.38 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 169 
 HIS   0.010   0.001   HIS B  82 
 PHE   0.019   0.002   PHE A 225 
 TYR   0.012   0.001   TYR A 507 
 ARG   0.007   0.000   ARG C 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04239 (  400)
  hydrogen bonds       : angle       4.83952 ( 1128)
  SS BOND              : bond        0.00461 (    3)
  SS BOND              : angle       0.71598 (    6)
  covalent geometry    : bond        0.00338 ( 8754)
  covalent geometry    : angle       0.54012 (11934)

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

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

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2222 Ramachandran restraints generated.
    1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 1.225 
Fit side-chains
REVERT: A  493 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7701 (mt)
REVERT: B  245 LEU cc_start: 0.7949 (mt) cc_final: 0.7688 (mp)
REVERT: E   68 PHE cc_start: 0.8222 (m-10) cc_final: 0.7966 (m-10)
  outliers start: 20
  outliers final: 19
  residues processed: 188
  average time/residue: 0.9261
  time to fit residues: 188.6935
Evaluate side-chains
  200 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 SER
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  508 ASN
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain B residue   24 ARG
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  145 LYS
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  268 ASN
Chi-restraints excluded: chain C residue  277 SER
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain E residue    7 SER
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   63 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 94 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9980
   chunk 105 optimal weight:    0.0570
   chunk 79 optimal weight:    3.9990
   chunk 10 optimal weight:    0.1980
   chunk 72 optimal weight:    0.3980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.4498

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

Flipped N/Q/H residues before XYZ refinement:
A 536 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.139908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.122078 restraints weight = 12293.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 1.79
r_work: 0.3491 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3351 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8757  Z= 0.148
  Angle     :  0.540   6.650  11940  Z= 0.289
  Chirality :  0.042   0.178   1392
  Planarity :  0.004   0.043   1500
  Dihedral  :  6.509  59.284   1293
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.61 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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:  0.48 (0.26), residues: 1111
  helix:  1.23 (0.28), residues: 367
  sheet:  0.37 (0.30), residues: 300
  loop : -0.38 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 169 
 HIS   0.010   0.001   HIS B  82 
 PHE   0.019   0.002   PHE A 225 
 TYR   0.012   0.001   TYR A 507 
 ARG   0.007   0.000   ARG C 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04239 (  400)
  hydrogen bonds       : angle       4.83952 ( 1128)
  SS BOND              : bond        0.00461 (    3)
  SS BOND              : angle       0.71598 (    6)
  covalent geometry    : bond        0.00338 ( 8754)
  covalent geometry    : angle       0.54012 (11934)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6915.36 seconds
wall clock time: 119 minutes 27.35 seconds (7167.35 seconds total)