Starting phenix.real_space_refine
on Thu Sep 18 12:27:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wsq_32764/09_2025/7wsq_32764.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wsq_32764/09_2025/7wsq_32764.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wsq_32764/09_2025/7wsq_32764.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wsq_32764/09_2025/7wsq_32764.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wsq_32764/09_2025/7wsq_32764.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wsq_32764/09_2025/7wsq_32764.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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: 6
    Type Number    sf(0)   Gaussians
     Fe     12      7.16       5
     P       4      5.49       5
     S      90      5.16       5
     C   10438      2.51       5
     N    2856      2.21       5
     O    3122      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16522
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 4143
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 537, 4143
          Classifications: {'peptide': 537}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 500}
    Chain: "B"
      Number of atoms: 780
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 780
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 3149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 418, 3149
          Classifications: {'peptide': 418}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 391}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 4143
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 537, 4143
          Classifications: {'peptide': 537}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 500}
    Chain: "E"
      Number of atoms: 780
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 780
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
          Chain breaks: 4
    Chain: "F"
      Number of atoms: 3149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 418, 3149
          Classifications: {'peptide': 418}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 391}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 60
          Unusual residues: {'F3S': 1, 'FAD': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 129
          Unusual residues: {'HEC': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 60
          Unusual residues: {'F3S': 1, 'FAD': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "F"
      Number of atoms: 129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 129
          Unusual residues: {'HEC': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1743  SG  CYS A 226      56.402  34.924  73.094  1.00 11.67           S
  ATOM   1714  SG  CYS A 222      54.539  31.327  76.966  1.00 16.07           S
  ATOM   1674  SG  CYS A 216      56.131  28.347  72.238  1.00 12.67           S
  ATOM   9815  SG  CYS D 226      49.725  95.575  73.082  1.00 12.69           S
  ATOM   9786  SG  CYS D 222      51.584  99.211  76.969  1.00 16.63           S
  ATOM   9746  SG  CYS D 216      50.012 102.154  72.238  1.00 15.48           S

  Time building chain proxies: 4.61, per 1000 atoms: 0.28
  Number of scatterers: 16522
  At special positions: 0
  Unit cell: (106.14, 131.37, 116.58, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe     12     26.01
     S      90     16.00
     P       4     15.00
     O    3122      8.00
     N    2856      7.00
     C   10438      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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=32, symmetry=0
  Number of additional bonds: simple=32, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.78
  Conformation dependent library (CDL) restraints added in 798.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" F3S A 602 "
        pdb="FE1  F3S A 602 " - pdb=" SG  CYS A 226 "
        pdb="FE4  F3S A 602 " - pdb=" SG  CYS A 216 "
        pdb="FE3  F3S A 602 " - pdb=" SG  CYS A 222 "
      pdb=" F3S D 602 "
        pdb="FE1  F3S D 602 " - pdb=" SG  CYS D 226 "
        pdb="FE4  F3S D 602 " - pdb=" SG  CYS D 216 "
        pdb="FE3  F3S D 602 " - pdb=" SG  CYS D 222 "
      Number of angles added : 18


  4144 Ramachandran restraints generated.
    2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3860

  Finding SS restraints...
    Secondary structure from input PDB file:
      82 helices and 16 sheets defined
      40.2% alpha, 6.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 30
    Processing helix  chain 'A' and resid 43 through 54
    Processing helix  chain 'A' and resid 56 through 61
      removed outlier: 3.975A  pdb=" N   GLN A  61 " --> pdb=" O   ASP A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 97
    Processing helix  chain 'A' and resid 105 through 110
    Processing helix  chain 'A' and resid 119 through 124
      removed outlier: 3.735A  pdb=" N   PHE A 123 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   LYS A 124 " --> pdb=" O   PRO A 120 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 119 through 124'
    Processing helix  chain 'A' and resid 124 through 130
    Processing helix  chain 'A' and resid 142 through 154
    Processing helix  chain 'A' and resid 181 through 195
    Processing helix  chain 'A' and resid 233 through 245
      removed outlier: 4.170A  pdb=" N   ALA A 237 " --> pdb=" O   ASN A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 301
    Processing helix  chain 'A' and resid 351 through 354
      removed outlier: 4.404A  pdb=" N   ASP A 354 " --> pdb=" O   ASN A 351 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 351 through 354'
    Processing helix  chain 'A' and resid 355 through 360
      removed outlier: 3.733A  pdb=" N   ARG A 358 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   SER A 359 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 384
    Processing helix  chain 'A' and resid 388 through 401
    Processing helix  chain 'A' and resid 440 through 462
      removed outlier: 4.573A  pdb=" N   VAL A 444 " --> pdb=" O   VAL A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 541
      removed outlier: 4.129A  pdb=" N   MET A 526 " --> pdb=" O   SER A 522 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   ASP A 535 " --> pdb=" O   LEU A 531 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ALA A 536 " --> pdb=" O   ARG A 532 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 56
    Processing helix  chain 'B' and resid 70 through 83
      removed outlier: 3.547A  pdb=" N   ALA B  74 " --> pdb=" O   ASN B  70 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   ALA B  81 " --> pdb=" O   LEU B  77 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLN B  82 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 98
      removed outlier: 3.553A  pdb=" N   ILE B  90 " --> pdb=" O   PHE B  86 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   LYS B  91 " --> pdb=" O   SER B  87 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ALA B  92 " --> pdb=" O   THR B  88 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   ARG B  94 " --> pdb=" O   ILE B  90 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   GLU B  95 " --> pdb=" O   LYS B  91 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   HIS B  96 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ILE B  97 " --> pdb=" O   LEU B  93 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   THR B  98 " --> pdb=" O   ARG B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 124
      No H-bonds generated for 'chain 'B' and resid 122 through 124'
    Processing helix  chain 'B' and resid 125 through 130
    Processing helix  chain 'C' and resid 41 through 50
    Processing helix  chain 'C' and resid 51 through 56
      removed outlier: 4.038A  pdb=" N   CYS C  55 " --> pdb=" O   ASP C  51 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   HIS C  56 " --> pdb=" O   CYS C  52 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 51 through 56'
    Processing helix  chain 'C' and resid 95 through 104
    Processing helix  chain 'C' and resid 122 through 126
      removed outlier: 3.776A  pdb=" N   ARG C 125 " --> pdb=" O   ALA C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 127 through 141
      removed outlier: 4.021A  pdb=" N   SER C 133 " --> pdb=" O   GLU C 129 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 160 through 162
      No H-bonds generated for 'chain 'C' and resid 160 through 162'
    Processing helix  chain 'C' and resid 163 through 172
      removed outlier: 3.811A  pdb=" N   TRP C 167 " --> pdb=" O   SER C 163 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ILE C 169 " --> pdb=" O   GLY C 165 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 185 through 197
      removed outlier: 3.666A  pdb=" N   GLU C 197 " --> pdb=" O   TYR C 193 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 200 through 206
      removed outlier: 4.068A  pdb=" N   CYS C 204 " --> pdb=" O   HIS C 200 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 245 through 256
    Processing helix  chain 'C' and resid 265 through 274
    Processing helix  chain 'C' and resid 275 through 278
    Processing helix  chain 'C' and resid 279 through 291
    Processing helix  chain 'C' and resid 334 through 343
      removed outlier: 3.714A  pdb=" N   VAL C 342 " --> pdb=" O   LEU C 338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 373 through 383
    Processing helix  chain 'C' and resid 408 through 423
    Processing helix  chain 'C' and resid 431 through 441
      removed outlier: 3.894A  pdb=" N   VAL C 435 " --> pdb=" O   SER C 431 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   LYS C 436 " --> pdb=" O   ALA C 432 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 445 through 451
      removed outlier: 3.540A  pdb=" N   LYS C 449 " --> pdb=" O   PRO C 446 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 452 through 471
      removed outlier: 3.555A  pdb=" N   MET C 456 " --> pdb=" O   SER C 452 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLY C 462 " --> pdb=" O   LEU C 458 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   VAL C 471 " --> pdb=" O   ALA C 467 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 16 through 30
    Processing helix  chain 'D' and resid 43 through 54
    Processing helix  chain 'D' and resid 56 through 61
      removed outlier: 3.887A  pdb=" N   GLN D  61 " --> pdb=" O   ASP D  57 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 92 through 97
    Processing helix  chain 'D' and resid 105 through 110
    Processing helix  chain 'D' and resid 119 through 124
      removed outlier: 3.758A  pdb=" N   PHE D 123 " --> pdb=" O   LEU D 119 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LYS D 124 " --> pdb=" O   PRO D 120 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 119 through 124'
    Processing helix  chain 'D' and resid 124 through 130
    Processing helix  chain 'D' and resid 138 through 154
      Proline residue:  D 144  - end of helix
    Processing helix  chain 'D' and resid 181 through 195
    Processing helix  chain 'D' and resid 234 through 245
    Processing helix  chain 'D' and resid 293 through 301
    Processing helix  chain 'D' and resid 351 through 354
      removed outlier: 4.456A  pdb=" N   ASP D 354 " --> pdb=" O   ASN D 351 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 351 through 354'
    Processing helix  chain 'D' and resid 355 through 360
      removed outlier: 3.724A  pdb=" N   ARG D 358 " --> pdb=" O   GLY D 355 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   SER D 359 " --> pdb=" O   ASP D 356 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 373 through 383
      removed outlier: 3.764A  pdb=" N   MET D 379 " --> pdb=" O   SER D 375 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 388 through 401
      removed outlier: 3.901A  pdb=" N   ASP D 392 " --> pdb=" O   GLY D 388 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLU D 393 " --> pdb=" O   LYS D 389 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 440 through 462
      removed outlier: 4.538A  pdb=" N   VAL D 444 " --> pdb=" O   VAL D 440 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ARG D 445 " --> pdb=" O   GLY D 441 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LYS D 446 " --> pdb=" O   GLU D 442 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   SER D 447 " --> pdb=" O   TYR D 443 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 522 through 541
      removed outlier: 4.031A  pdb=" N   MET D 526 " --> pdb=" O   SER D 522 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ALA D 534 " --> pdb=" O   SER D 530 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ASP D 535 " --> pdb=" O   LEU D 531 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ALA D 536 " --> pdb=" O   ARG D 532 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 56
    Processing helix  chain 'E' and resid 70 through 83
      removed outlier: 3.583A  pdb=" N   ALA E  74 " --> pdb=" O   ASN E  70 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   ALA E  81 " --> pdb=" O   LEU E  77 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLN E  82 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 98
      removed outlier: 3.558A  pdb=" N   ILE E  90 " --> pdb=" O   PHE E  86 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   LYS E  91 " --> pdb=" O   SER E  87 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ALA E  92 " --> pdb=" O   THR E  88 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   ARG E  94 " --> pdb=" O   ILE E  90 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   GLU E  95 " --> pdb=" O   LYS E  91 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   HIS E  96 " --> pdb=" O   ALA E  92 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ILE E  97 " --> pdb=" O   LEU E  93 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR E  98 " --> pdb=" O   ARG E  94 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 124
      No H-bonds generated for 'chain 'E' and resid 122 through 124'
    Processing helix  chain 'E' and resid 125 through 130
    Processing helix  chain 'F' and resid 41 through 50
      removed outlier: 3.501A  pdb=" N   LEU F  46 " --> pdb=" O   ARG F  42 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 51 through 56
      removed outlier: 4.039A  pdb=" N   CYS F  55 " --> pdb=" O   ASP F  51 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   HIS F  56 " --> pdb=" O   CYS F  52 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 51 through 56'
    Processing helix  chain 'F' and resid 95 through 104
    Processing helix  chain 'F' and resid 122 through 126
      removed outlier: 3.772A  pdb=" N   ARG F 125 " --> pdb=" O   ALA F 122 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 127 through 141
      removed outlier: 4.021A  pdb=" N   SER F 133 " --> pdb=" O   GLU F 129 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 160 through 162
      No H-bonds generated for 'chain 'F' and resid 160 through 162'
    Processing helix  chain 'F' and resid 163 through 172
      removed outlier: 3.758A  pdb=" N   TRP F 167 " --> pdb=" O   SER F 163 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ILE F 169 " --> pdb=" O   GLY F 165 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 185 through 197
      removed outlier: 3.667A  pdb=" N   GLU F 197 " --> pdb=" O   TYR F 193 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 200 through 206
      removed outlier: 4.069A  pdb=" N   CYS F 204 " --> pdb=" O   HIS F 200 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 245 through 256
    Processing helix  chain 'F' and resid 265 through 274
    Processing helix  chain 'F' and resid 275 through 278
    Processing helix  chain 'F' and resid 279 through 291
    Processing helix  chain 'F' and resid 334 through 341
    Processing helix  chain 'F' and resid 373 through 383
    Processing helix  chain 'F' and resid 408 through 423
    Processing helix  chain 'F' and resid 431 through 441
      removed outlier: 3.891A  pdb=" N   VAL F 435 " --> pdb=" O   SER F 431 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   LYS F 436 " --> pdb=" O   ALA F 432 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 445 through 451
      removed outlier: 3.539A  pdb=" N   LYS F 449 " --> pdb=" O   PRO F 446 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 452 through 471
      removed outlier: 3.564A  pdb=" N   MET F 456 " --> pdb=" O   SER F 452 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL F 471 " --> pdb=" O   ALA F 467 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 249
      removed outlier: 6.607A  pdb=" N   VAL A  33 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
      removed outlier: 8.096A  pdb=" N   ILE A 249 " --> pdb=" O   VAL A  33 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   LEU A  35 " --> pdb=" O   ILE A 249 " (cutoff:3.500A)
      removed outlier: 5.854A  pdb=" N   VAL A  11 " --> pdb=" O   VAL A 286 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   PHE A 285 " --> pdb=" O   PHE A 507 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 89
      removed outlier: 6.386A  pdb=" N   ILE A  87 " --> pdb=" O   VAL A 436 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   HIS A 433 " --> pdb=" O   SER A 422 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 200
    Processing sheet with id=AA4, first strand: chain 'A' and resid 253 through 258
      removed outlier: 7.328A  pdb=" N   SER A 269 " --> pdb=" O   TYR A 255 " (cutoff:3.500A)
      removed outlier: 4.839A  pdb=" N   MET A 257 " --> pdb=" O   ALA A 267 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   ALA A 267 " --> pdb=" O   MET A 257 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 332
      removed outlier: 3.540A  pdb=" N   ILE A 405 " --> pdb=" O   MET A 329 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   ASP A 404 " --> pdb=" O   ASN A 369 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 70 through 73
      removed outlier: 3.506A  pdb=" N   ILE C  71 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ILE C  78 " --> pdb=" O   ILE C  71 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 224 through 225
    Processing sheet with id=AA8, first strand: chain 'C' and resid 385 through 388
    Processing sheet with id=AA9, first strand: chain 'D' and resid 247 through 249
      removed outlier: 6.607A  pdb=" N   VAL D  33 " --> pdb=" O   LYS D 247 " (cutoff:3.500A)
      removed outlier: 8.096A  pdb=" N   ILE D 249 " --> pdb=" O   VAL D  33 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   LEU D  35 " --> pdb=" O   ILE D 249 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   VAL D  11 " --> pdb=" O   VAL D 286 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   PHE D 285 " --> pdb=" O   PHE D 507 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 87 through 89
      removed outlier: 6.379A  pdb=" N   ILE D  87 " --> pdb=" O   VAL D 436 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   HIS D 433 " --> pdb=" O   SER D 422 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 198 through 200
    Processing sheet with id=AB3, first strand: chain 'D' and resid 253 through 258
      removed outlier: 7.279A  pdb=" N   SER D 269 " --> pdb=" O   TYR D 255 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   MET D 257 " --> pdb=" O   ALA D 267 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   ALA D 267 " --> pdb=" O   MET D 257 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 329 through 332
      removed outlier: 4.528A  pdb=" N   ASP D 404 " --> pdb=" O   ASN D 369 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 70 through 73
      removed outlier: 3.505A  pdb=" N   ILE F  71 " --> pdb=" O   ILE F  78 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE F  78 " --> pdb=" O   ILE F  71 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'F' and resid 224 through 225
    Processing sheet with id=AB7, first strand: chain 'F' and resid 385 through 388

    513 hydrogen bonds defined for protein.
    1431 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: 2.54

  Time building geometry restraints manager: 2.32 seconds

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

  Histogram of bond lengths:
        1.22 -     1.83: 16930
        1.83 -     2.45: 36
        2.45 -     3.06: 0
        3.06 -     3.68: 0
        3.68 -     4.29: 6
  Bond restraints: 16972
  Sorted by residual:
  bond pdb=" S4  F3S A 602 "
       pdb="FE1  F3S A 602 "
    ideal  model  delta    sigma   weight residual
    2.233  4.268 -2.035 2.00e-02 2.50e+03 1.04e+04
  bond pdb=" S4  F3S D 602 "
       pdb="FE1  F3S D 602 "
    ideal  model  delta    sigma   weight residual
    2.233  4.268 -2.035 2.00e-02 2.50e+03 1.04e+04
  bond pdb=" S1  F3S A 602 "
       pdb="FE4  F3S A 602 "
    ideal  model  delta    sigma   weight residual
    2.258  4.291 -2.033 2.00e-02 2.50e+03 1.03e+04
  bond pdb=" S1  F3S D 602 "
       pdb="FE4  F3S D 602 "
    ideal  model  delta    sigma   weight residual
    2.258  4.290 -2.032 2.00e-02 2.50e+03 1.03e+04
  bond pdb=" S2  F3S A 602 "
       pdb="FE3  F3S A 602 "
    ideal  model  delta    sigma   weight residual
    2.300  4.248 -1.948 2.00e-02 2.50e+03 9.49e+03
  ... (remaining 16967 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    15.48: 23172
       15.48 -    30.96: 24
       30.96 -    46.45: 2
       46.45 -    61.93: 0
       61.93 -    77.41: 4
  Bond angle restraints: 23202
  Sorted by residual:
  angle pdb=" S1  F3S A 602 "
        pdb="FE4  F3S A 602 "
        pdb=" S3  F3S A 602 "
      ideal   model   delta    sigma   weight residual
     114.75   37.34   77.41 3.00e+00 1.11e-01 6.66e+02
  angle pdb=" S1  F3S D 602 "
        pdb="FE4  F3S D 602 "
        pdb=" S3  F3S D 602 "
      ideal   model   delta    sigma   weight residual
     114.75   37.36   77.39 3.00e+00 1.11e-01 6.65e+02
  angle pdb=" S3  F3S A 602 "
        pdb="FE1  F3S A 602 "
        pdb=" S4  F3S A 602 "
      ideal   model   delta    sigma   weight residual
     112.59   38.05   74.54 3.00e+00 1.11e-01 6.17e+02
  angle pdb=" S3  F3S D 602 "
        pdb="FE1  F3S D 602 "
        pdb=" S4  F3S D 602 "
      ideal   model   delta    sigma   weight residual
     112.59   38.07   74.52 3.00e+00 1.11e-01 6.17e+02
  angle pdb=" S1  F3S D 602 "
        pdb="FE4  F3S D 602 "
        pdb=" S2  F3S D 602 "
      ideal   model   delta    sigma   weight residual
     103.63   72.19   31.44 3.00e+00 1.11e-01 1.10e+02
  ... (remaining 23197 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.27: 9275
       22.27 -    44.53: 609
       44.53 -    66.80: 70
       66.80 -    89.06: 26
       89.06 -   111.33: 2
  Dihedral angle restraints: 9982
    sinusoidal: 3928
      harmonic: 6054
  Sorted by residual:
  dihedral pdb=" CA  HIS E 118 "
           pdb=" C   HIS E 118 "
           pdb=" N   PRO E 119 "
           pdb=" CA  PRO E 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  133.29   46.71     0      5.00e+00 4.00e-02 8.73e+01
  dihedral pdb=" CA  HIS B 118 "
           pdb=" C   HIS B 118 "
           pdb=" N   PRO B 119 "
           pdb=" CA  PRO B 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  134.44   45.56     0      5.00e+00 4.00e-02 8.30e+01
  dihedral pdb=" CA  PHE D  80 "
           pdb=" C   PHE D  80 "
           pdb=" N   PRO D  81 "
           pdb=" CA  PRO D  81 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -140.76  -39.24     0      5.00e+00 4.00e-02 6.16e+01
  ... (remaining 9979 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    3.128: 2476
       3.128 -    6.256: 0
       6.256 -    9.384: 0
       9.384 -   12.512: 0
      12.512 -   15.640: 2
  Chirality restraints: 2478
  Sorted by residual:
  chirality pdb=" S2  F3S D 602 "
            pdb="FE1  F3S D 602 "
            pdb="FE3  F3S D 602 "
            pdb="FE4  F3S D 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     10.77   -4.87   15.64 2.00e-01 2.50e+01 6.12e+03
  chirality pdb=" S2  F3S A 602 "
            pdb="FE1  F3S A 602 "
            pdb="FE3  F3S A 602 "
            pdb="FE4  F3S A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     10.77   -4.87   15.64 2.00e-01 2.50e+01 6.11e+03
  chirality pdb=" CB  ILE B 133 "
            pdb=" CA  ILE B 133 "
            pdb=" CG1 ILE B 133 "
            pdb=" CG2 ILE B 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.51e+00
  ... (remaining 2475 not shown)

  Planarity restraints: 2986
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CBD HEC F 501 "   -0.023 2.00e-02 2.50e+03   4.93e-02 2.43e+01
        pdb=" CGD HEC F 501 "    0.085 2.00e-02 2.50e+03
        pdb=" O1D HEC F 501 "   -0.030 2.00e-02 2.50e+03
        pdb=" O2D HEC F 501 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CBD HEC C 501 "   -0.023 2.00e-02 2.50e+03   4.90e-02 2.40e+01
        pdb=" CGD HEC C 501 "    0.085 2.00e-02 2.50e+03
        pdb=" O1D HEC C 501 "   -0.030 2.00e-02 2.50e+03
        pdb=" O2D HEC C 501 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 111 "   -0.029 2.00e-02 2.50e+03   2.95e-02 2.17e+01
        pdb=" CG  TRP A 111 "    0.078 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 111 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 111 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 111 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 111 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 111 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 111 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 111 "   -0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 111 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 2983 not shown)

  Histogram of nonbonded interaction distances:
        1.83 -     2.44: 100
        2.44 -     3.06: 11043
        3.06 -     3.67: 26340
        3.67 -     4.29: 38200
        4.29 -     4.90: 61868
  Nonbonded interactions: 137551
  Sorted by model distance:
  nonbonded pdb=" SG  CYS A 226 "
            pdb=" S1  F3S A 602 "
     model   vdw
     1.827 3.760
  nonbonded pdb=" SG  CYS D 226 "
            pdb=" S1  F3S D 602 "
     model   vdw
     1.850 3.760
  nonbonded pdb=" CG  ASN D 521 "
            pdb=" C4  FAD D 601 "
     model   vdw
     2.070 2.792
  nonbonded pdb=" CG  ASN A 521 "
            pdb=" C4  FAD A 601 "
     model   vdw
     2.079 2.792
  nonbonded pdb=" O   ARG A 358 "
            pdb=" OH  TYR A 443 "
     model   vdw
     2.112 3.040
  ... (remaining 137546 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     19.210
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
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      :  0.039   2.035  17010  Z= 1.954
  Angle     :  1.699  77.412  23220  Z= 0.565
  Chirality :  0.446  15.640   2478
  Planarity :  0.006   0.065   2986
  Dihedral  : 14.723 111.326   6122
  Min Nonbonded Distance : 1.827

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.66 (0.19), residues: 2072
  helix:  0.35 (0.21), residues: 646
  sheet:  0.17 (0.43), residues: 176
  loop : -0.96 (0.18), residues: 1250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 396 
 TYR   0.032   0.001   TYR D  79 
 PHE   0.015   0.001   PHE B 144 
 TRP   0.078   0.002   TRP A 111 
 HIS   0.006   0.001   HIS B 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.03848 (16972)
  covalent geometry    : angle       1.52060 (23202)
  hydrogen bonds       : bond        0.25501 (  513)
  hydrogen bonds       : angle       8.25616 ( 1431)
  metal coordination   : bond        0.00232 (    6)
  metal coordination   : angle      27.24183 (   18)
  Misc. bond           : bond        0.09011 (   32)

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

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

  4144 Ramachandran restraints generated.
    2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4144 Ramachandran restraints generated.
    2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 273
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 LYS cc_start: 0.5338 (ttmm) cc_final: 0.5090 (mtpp)
REVERT: A  321 MET cc_start: 0.7044 (tpp) cc_final: 0.6784 (mmt)
REVERT: C  130 ASP cc_start: 0.7306 (m-30) cc_final: 0.7101 (m-30)
REVERT: C  352 LYS cc_start: 0.8330 (mmtt) cc_final: 0.8002 (tppt)
REVERT: D  321 MET cc_start: 0.7370 (tpp) cc_final: 0.7095 (mmt)
REVERT: D  329 MET cc_start: 0.7587 (tpp) cc_final: 0.7208 (mtp)
REVERT: F  130 ASP cc_start: 0.7282 (m-30) cc_final: 0.7078 (m-30)
REVERT: F  352 LYS cc_start: 0.8300 (mmtt) cc_final: 0.7964 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 273
  average time/residue: 0.1109
  time to fit residues: 47.4220
Evaluate side-chains
  213 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 194 optimal weight:    1.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:   10.0000
   chunk 200 optimal weight:    7.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    6.9990
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 165 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.166931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.143589 restraints weight = 25525.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.143979 restraints weight = 26754.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.145800 restraints weight = 21706.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.145717 restraints weight = 16128.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.146024 restraints weight = 15985.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.1380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.142  17010  Z= 0.223
  Angle     :  1.619  89.618  23220  Z= 0.473
  Chirality :  0.062   1.468   2478
  Planarity :  0.006   0.063   2986
  Dihedral  :  9.741 104.067   2432
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.66 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 13.03 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.61 (0.19), residues: 2072
  helix:  0.51 (0.20), residues: 696
  sheet:  0.10 (0.43), residues: 180
  loop : -1.05 (0.18), residues: 1196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 499 
 TYR   0.025   0.002   TYR D  79 
 PHE   0.018   0.002   PHE C  64 
 TRP   0.041   0.002   TRP A 111 
 HIS   0.009   0.001   HIS A 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00536 (16972)
  covalent geometry    : angle       1.17040 (23202)
  hydrogen bonds       : bond        0.04613 (  513)
  hydrogen bonds       : angle       5.93527 ( 1431)
  metal coordination   : bond        0.01386 (    6)
  metal coordination   : angle      40.21568 (   18)
  Misc. bond           : bond        0.03532 (   32)

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

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

  4144 Ramachandran restraints generated.
    2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4144 Ramachandran restraints generated.
    2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 233
  time to evaluate  : 0.639 
Fit side-chains
REVERT: A  156 MET cc_start: 0.8333 (ttm) cc_final: 0.8081 (mtp)
REVERT: C  352 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8190 (tppt)
REVERT: D  329 MET cc_start: 0.7562 (tpp) cc_final: 0.7221 (ttt)
REVERT: F  352 LYS cc_start: 0.8432 (mmtt) cc_final: 0.8165 (tppt)
  outliers start: 16
  outliers final: 14
  residues processed: 238
  average time/residue: 0.1168
  time to fit residues: 43.3580
Evaluate side-chains
  229 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 215
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  169 TYR
Chi-restraints excluded: chain C residue  345 SER
Chi-restraints excluded: chain D residue  268 ILE
Chi-restraints excluded: chain D residue  292 ILE
Chi-restraints excluded: chain D residue  458 ILE
Chi-restraints excluded: chain E residue   93 LEU
Chi-restraints excluded: chain E residue  133 ILE
Chi-restraints excluded: chain F residue  345 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 121 optimal weight:    0.9980
   chunk 126 optimal weight:    1.9990
   chunk 58 optimal weight:    0.3980
   chunk 61 optimal weight:    0.7980
   chunk 157 optimal weight:   20.0000
   chunk 33 optimal weight:   10.0000
   chunk 178 optimal weight:    4.9990
   chunk 145 optimal weight:    9.9990
   chunk 169 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   chunk 72 optimal weight:   20.0000
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 219 ASN
B 118 HIS
C  58 ASN
** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 219 ASN
E 118 HIS
F  58 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.170149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.145611 restraints weight = 25313.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.146367 restraints weight = 22445.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.147845 restraints weight = 20198.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.148172 restraints weight = 14332.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.148466 restraints weight = 14435.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.102  17010  Z= 0.166
  Angle     :  1.492  83.988  23220  Z= 0.433
  Chirality :  0.060   1.424   2478
  Planarity :  0.005   0.061   2986
  Dihedral  :  9.606 104.362   2432
  Min Nonbonded Distance : 1.809

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 15.96 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.49 (0.19), residues: 2072
  helix:  0.65 (0.21), residues: 698
  sheet: -0.13 (0.41), residues: 180
  loop : -0.95 (0.18), residues: 1194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 396 
 TYR   0.027   0.002   TYR D  79 
 PHE   0.011   0.001   PHE B 144 
 TRP   0.027   0.001   TRP A 111 
 HIS   0.006   0.001   HIS A 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (16972)
  covalent geometry    : angle       1.10376 (23202)
  hydrogen bonds       : bond        0.03443 (  513)
  hydrogen bonds       : angle       5.40065 ( 1431)
  metal coordination   : bond        0.00501 (    6)
  metal coordination   : angle      36.09602 (   18)
  Misc. bond           : bond        0.01588 (   32)

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

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

  4144 Ramachandran restraints generated.
    2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4144 Ramachandran restraints generated.
    2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 247
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 MET cc_start: 0.8269 (ttm) cc_final: 0.7989 (mtp)
REVERT: A  221 ASN cc_start: 0.8852 (t0) cc_final: 0.8449 (t0)
REVERT: A  329 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7368 (mtp)
REVERT: A  523 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8959 (t)
REVERT: C  187 ASP cc_start: 0.7467 (t70) cc_final: 0.7193 (t70)
REVERT: C  352 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8188 (tppt)
REVERT: D  221 ASN cc_start: 0.8860 (t0) cc_final: 0.8461 (t0)
REVERT: F  124 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8314 (t0)
REVERT: F  352 LYS cc_start: 0.8404 (mmtt) cc_final: 0.8159 (tppt)
  outliers start: 31
  outliers final: 14
  residues processed: 268
  average time/residue: 0.1238
  time to fit residues: 52.1976
Evaluate side-chains
  238 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 221
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  523 THR
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  169 TYR
Chi-restraints excluded: chain C residue  375 ASP
Chi-restraints excluded: chain C residue  384 VAL
Chi-restraints excluded: chain D residue   60 SER
Chi-restraints excluded: chain D residue  411 VAL
Chi-restraints excluded: chain D residue  493 VAL
Chi-restraints excluded: chain E residue   93 LEU
Chi-restraints excluded: chain E residue  133 ILE
Chi-restraints excluded: chain F residue  124 ASN
Chi-restraints excluded: chain F residue  384 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 120 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 190 optimal weight:    9.9990
   chunk 45 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 201 optimal weight:    4.9990
   chunk 187 optimal weight:    0.7980
   chunk 159 optimal weight:    5.9990
   chunk 147 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 345 GLN
** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 427 GLN
E 165 ASN
** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 427 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.168169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.146490 restraints weight = 25028.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.146565 restraints weight = 27217.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.148443 restraints weight = 23378.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.148404 restraints weight = 17436.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.148750 restraints weight = 15509.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.103  17010  Z= 0.153
  Angle     :  1.457  83.888  23220  Z= 0.426
  Chirality :  0.060   1.443   2478
  Planarity :  0.005   0.060   2986
  Dihedral  :  9.480 102.164   2432
  Min Nonbonded Distance : 1.798

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.31 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.19), residues: 2072
  helix:  0.61 (0.20), residues: 710
  sheet: -0.28 (0.40), residues: 180
  loop : -0.88 (0.18), residues: 1182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 396 
 TYR   0.025   0.002   TYR D  79 
 PHE   0.015   0.001   PHE F  64 
 TRP   0.020   0.001   TRP A 111 
 HIS   0.008   0.001   HIS C 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (16972)
  covalent geometry    : angle       1.08916 (23202)
  hydrogen bonds       : bond        0.03092 (  513)
  hydrogen bonds       : angle       5.24179 ( 1431)
  metal coordination   : bond        0.00354 (    6)
  metal coordination   : angle      34.78794 (   18)
  Misc. bond           : bond        0.00935 (   32)

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

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

  4144 Ramachandran restraints generated.
    2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4144 Ramachandran restraints generated.
    2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 229
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 MET cc_start: 0.8352 (ttm) cc_final: 0.7976 (mtp)
REVERT: A  221 ASN cc_start: 0.8785 (t0) cc_final: 0.8407 (t0)
REVERT: A  329 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7548 (mtp)
REVERT: C  352 LYS cc_start: 0.8414 (mmtt) cc_final: 0.8157 (tppt)
REVERT: D   98 GLN cc_start: 0.7621 (pp30) cc_final: 0.7408 (pp30)
REVERT: D  221 ASN cc_start: 0.8791 (t0) cc_final: 0.8407 (t0)
REVERT: D  329 MET cc_start: 0.7401 (ttm) cc_final: 0.7141 (ttt)
REVERT: D  526 MET cc_start: 0.7717 (mtm) cc_final: 0.7428 (mtm)
REVERT: F  124 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8286 (t0)
REVERT: F  352 LYS cc_start: 0.8348 (mmtt) cc_final: 0.8105 (tppt)
  outliers start: 35
  outliers final: 21
  residues processed: 249
  average time/residue: 0.1211
  time to fit residues: 48.2080
Evaluate side-chains
  238 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 215
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  149 MET
Chi-restraints excluded: chain B residue  169 TYR
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  345 SER
Chi-restraints excluded: chain C residue  375 ASP
Chi-restraints excluded: chain D residue   60 SER
Chi-restraints excluded: chain D residue   87 ILE
Chi-restraints excluded: chain D residue  253 VAL
Chi-restraints excluded: chain D residue  292 ILE
Chi-restraints excluded: chain D residue  337 ILE
Chi-restraints excluded: chain D residue  411 VAL
Chi-restraints excluded: chain D residue  493 VAL
Chi-restraints excluded: chain E residue  133 ILE
Chi-restraints excluded: chain E residue  149 MET
Chi-restraints excluded: chain E residue  159 ILE
Chi-restraints excluded: chain F residue  124 ASN
Chi-restraints excluded: chain F residue  293 VAL
Chi-restraints excluded: chain F residue  345 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 154 optimal weight:   10.0000
   chunk 167 optimal weight:   10.0000
   chunk 163 optimal weight:    7.9990
   chunk 200 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 141 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 119 optimal weight:    3.9990
   chunk 147 optimal weight:    3.9990
   chunk 72 optimal weight:   20.0000
   chunk 55 optimal weight:    9.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** C 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 263 ASN
D 503 HIS
** F 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.159288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.135531 restraints weight = 25666.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.136329 restraints weight = 23921.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.137699 restraints weight = 20671.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.137837 restraints weight = 15262.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.137984 restraints weight = 14908.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.2690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.340  17010  Z= 0.334
  Angle     :  1.659  84.279  23220  Z= 0.512
  Chirality :  0.067   1.525   2478
  Planarity :  0.007   0.066   2986
  Dihedral  : 10.272 118.422   2432
  Min Nonbonded Distance : 1.809

Molprobity Statistics.
  All-atom Clashscore : 15.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 16.61 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.07 (0.18), residues: 2072
  helix:  0.12 (0.20), residues: 716
  sheet: -0.39 (0.40), residues: 184
  loop : -1.32 (0.18), residues: 1172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 396 
 TYR   0.024   0.003   TYR D  79 
 PHE   0.019   0.003   PHE B 144 
 TRP   0.022   0.002   TRP D 111 
 HIS   0.006   0.002   HIS D 478 

Details of bonding type rmsd
  covalent geometry    : bond        0.00790 (16972)
  covalent geometry    : angle       1.25093 (23202)
  hydrogen bonds       : bond        0.04029 (  513)
  hydrogen bonds       : angle       5.70085 ( 1431)
  metal coordination   : bond        0.00550 (    6)
  metal coordination   : angle      39.17784 (   18)
  Misc. bond           : bond        0.08509 (   32)

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

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

  4144 Ramachandran restraints generated.
    2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4144 Ramachandran restraints generated.
    2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 216
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 MET cc_start: 0.8420 (ttm) cc_final: 0.8134 (mtp)
REVERT: A  329 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7484 (mtp)
REVERT: B  134 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7061 (tt0)
REVERT: C  124 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8524 (t0)
REVERT: D  184 ASP cc_start: 0.7183 (m-30) cc_final: 0.6937 (m-30)
REVERT: D  329 MET cc_start: 0.7490 (ttm) cc_final: 0.7106 (ttt)
REVERT: D  352 PHE cc_start: 0.8320 (m-80) cc_final: 0.8092 (m-80)
REVERT: D  368 TYR cc_start: 0.7983 (OUTLIER) cc_final: 0.7092 (p90)
REVERT: F  124 ASN cc_start: 0.8866 (OUTLIER) cc_final: 0.8463 (t0)
  outliers start: 77
  outliers final: 56
  residues processed: 272
  average time/residue: 0.1205
  time to fit residues: 52.5651
Evaluate side-chains
  260 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 199
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  368 TYR
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain A residue  469 MET
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  507 PHE
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  134 GLU
Chi-restraints excluded: chain B residue  149 MET
Chi-restraints excluded: chain B residue  159 ILE
Chi-restraints excluded: chain B residue  169 TYR
Chi-restraints excluded: chain C residue   64 PHE
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  124 ASN
Chi-restraints excluded: chain C residue  187 ASP
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  345 SER
Chi-restraints excluded: chain C residue  375 ASP
Chi-restraints excluded: chain C residue  384 VAL
Chi-restraints excluded: chain C residue  393 ILE
Chi-restraints excluded: chain D residue   13 ILE
Chi-restraints excluded: chain D residue   60 SER
Chi-restraints excluded: chain D residue   87 ILE
Chi-restraints excluded: chain D residue  146 TYR
Chi-restraints excluded: chain D residue  253 VAL
Chi-restraints excluded: chain D residue  268 ILE
Chi-restraints excluded: chain D residue  294 THR
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  316 LEU
Chi-restraints excluded: chain D residue  337 ILE
Chi-restraints excluded: chain D residue  368 TYR
Chi-restraints excluded: chain D residue  411 VAL
Chi-restraints excluded: chain D residue  420 VAL
Chi-restraints excluded: chain D residue  429 LEU
Chi-restraints excluded: chain D residue  458 ILE
Chi-restraints excluded: chain D residue  470 THR
Chi-restraints excluded: chain D residue  493 VAL
Chi-restraints excluded: chain E residue   93 LEU
Chi-restraints excluded: chain E residue  133 ILE
Chi-restraints excluded: chain E residue  149 MET
Chi-restraints excluded: chain E residue  159 ILE
Chi-restraints excluded: chain F residue   64 PHE
Chi-restraints excluded: chain F residue  103 LEU
Chi-restraints excluded: chain F residue  124 ASN
Chi-restraints excluded: chain F residue  187 ASP
Chi-restraints excluded: chain F residue  293 VAL
Chi-restraints excluded: chain F residue  345 SER
Chi-restraints excluded: chain F residue  384 VAL
Chi-restraints excluded: chain F residue  393 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 164 optimal weight:    3.9990
   chunk 92 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 106 optimal weight:    4.9990
   chunk 170 optimal weight:    0.9980
   chunk 172 optimal weight:    0.0670
   chunk 84 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 110 optimal weight:    7.9990
   overall best weight:    0.7920

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

Flipped N/Q/H residues before XYZ refinement:
** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 425 ASN
D  46 GLN
** D 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 118 HIS
F 425 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.167597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.144663 restraints weight = 25346.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.145058 restraints weight = 26518.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.146681 restraints weight = 22046.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.147201 restraints weight = 16084.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.147423 restraints weight = 16311.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.104  17010  Z= 0.149
  Angle     :  1.469  84.319  23220  Z= 0.433
  Chirality :  0.059   1.396   2478
  Planarity :  0.005   0.062   2986
  Dihedral  :  9.774 112.565   2432
  Min Nonbonded Distance : 1.798

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 18.25 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.66 (0.19), residues: 2072
  helix:  0.47 (0.20), residues: 724
  sheet: -0.44 (0.40), residues: 184
  loop : -1.02 (0.19), residues: 1164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 205 
 TYR   0.025   0.002   TYR A  79 
 PHE   0.024   0.001   PHE C 306 
 TRP   0.020   0.001   TRP A 111 
 HIS   0.007   0.001   HIS A 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (16972)
  covalent geometry    : angle       1.11396 (23202)
  hydrogen bonds       : bond        0.02985 (  513)
  hydrogen bonds       : angle       5.18284 ( 1431)
  metal coordination   : bond        0.00343 (    6)
  metal coordination   : angle      34.39983 (   18)
  Misc. bond           : bond        0.01284 (   32)

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

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

  4144 Ramachandran restraints generated.
    2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4144 Ramachandran restraints generated.
    2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 225
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 GLN cc_start: 0.7789 (pp30) cc_final: 0.7362 (pp30)
REVERT: A  156 MET cc_start: 0.8423 (ttm) cc_final: 0.8074 (mtp)
REVERT: A  221 ASN cc_start: 0.8812 (t0) cc_final: 0.8433 (t0)
REVERT: A  329 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7262 (mtp)
REVERT: C  124 ASN cc_start: 0.8760 (OUTLIER) cc_final: 0.8475 (t0)
REVERT: C  352 LYS cc_start: 0.8428 (mmtt) cc_final: 0.8152 (tppt)
REVERT: D   98 GLN cc_start: 0.7771 (pp30) cc_final: 0.7494 (pp30)
REVERT: D  221 ASN cc_start: 0.8860 (t0) cc_final: 0.8459 (t0)
REVERT: D  329 MET cc_start: 0.7289 (ttm) cc_final: 0.6939 (ttt)
REVERT: D  368 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.6189 (p90)
REVERT: F  352 LYS cc_start: 0.8392 (mmtt) cc_final: 0.8114 (tppt)
  outliers start: 58
  outliers final: 38
  residues processed: 261
  average time/residue: 0.1249
  time to fit residues: 51.5513
Evaluate side-chains
  250 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 209
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  502 ASP
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  149 MET
Chi-restraints excluded: chain B residue  169 TYR
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain C residue  124 ASN
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  302 THR
Chi-restraints excluded: chain C residue  345 SER
Chi-restraints excluded: chain C residue  375 ASP
Chi-restraints excluded: chain C residue  384 VAL
Chi-restraints excluded: chain C residue  425 ASN
Chi-restraints excluded: chain D residue   60 SER
Chi-restraints excluded: chain D residue   87 ILE
Chi-restraints excluded: chain D residue  137 MET
Chi-restraints excluded: chain D residue  146 TYR
Chi-restraints excluded: chain D residue  253 VAL
Chi-restraints excluded: chain D residue  337 ILE
Chi-restraints excluded: chain D residue  368 TYR
Chi-restraints excluded: chain D residue  411 VAL
Chi-restraints excluded: chain D residue  420 VAL
Chi-restraints excluded: chain D residue  429 LEU
Chi-restraints excluded: chain D residue  493 VAL
Chi-restraints excluded: chain E residue   93 LEU
Chi-restraints excluded: chain E residue  133 ILE
Chi-restraints excluded: chain E residue  149 MET
Chi-restraints excluded: chain F residue  293 VAL
Chi-restraints excluded: chain F residue  302 THR
Chi-restraints excluded: chain F residue  345 SER
Chi-restraints excluded: chain F residue  384 VAL
Chi-restraints excluded: chain F residue  425 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 89 optimal weight:   30.0000
   chunk 3 optimal weight:    0.9980
   chunk 131 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 168 optimal weight:    0.9990
   chunk 8 optimal weight:   10.0000
   chunk 83 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 120 optimal weight:    5.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 425 ASN
F 425 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.169022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.147267 restraints weight = 25310.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.147305 restraints weight = 25658.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.149029 restraints weight = 22511.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.148980 restraints weight = 16944.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.149083 restraints weight = 16376.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.2623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.103  17010  Z= 0.147
  Angle     :  1.445  83.868  23220  Z= 0.426
  Chirality :  0.060   1.436   2478
  Planarity :  0.005   0.061   2986
  Dihedral  :  9.444 106.456   2432
  Min Nonbonded Distance : 1.795

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 19.60 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.55 (0.19), residues: 2072
  helix:  0.58 (0.20), residues: 722
  sheet: -0.51 (0.40), residues: 184
  loop : -0.94 (0.19), residues: 1166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 396 
 TYR   0.045   0.002   TYR A  79 
 PHE   0.019   0.001   PHE C 306 
 TRP   0.017   0.001   TRP D 497 
 HIS   0.007   0.001   HIS E  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (16972)
  covalent geometry    : angle       1.09351 (23202)
  hydrogen bonds       : bond        0.02860 (  513)
  hydrogen bonds       : angle       5.02253 ( 1431)
  metal coordination   : bond        0.00388 (    6)
  metal coordination   : angle      33.92215 (   18)
  Misc. bond           : bond        0.02079 (   32)

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

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

  4144 Ramachandran restraints generated.
    2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4144 Ramachandran restraints generated.
    2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 223
  time to evaluate  : 0.665 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 GLN cc_start: 0.7623 (pp30) cc_final: 0.7406 (pp30)
REVERT: A  109 TRP cc_start: 0.7996 (m100) cc_final: 0.7776 (m100)
REVERT: A  156 MET cc_start: 0.8329 (ttm) cc_final: 0.7863 (mtp)
REVERT: A  221 ASN cc_start: 0.8759 (t0) cc_final: 0.8426 (t0)
REVERT: A  329 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7403 (mtp)
REVERT: C  124 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8487 (t0)
REVERT: C  352 LYS cc_start: 0.8380 (mmtt) cc_final: 0.8094 (tppt)
REVERT: D   98 GLN cc_start: 0.7784 (pp30) cc_final: 0.7453 (pp30)
REVERT: D  221 ASN cc_start: 0.8785 (t0) cc_final: 0.8416 (t0)
REVERT: D  242 GLU cc_start: 0.6602 (mt-10) cc_final: 0.6385 (mt-10)
REVERT: D  329 MET cc_start: 0.7358 (ttm) cc_final: 0.6983 (ttt)
REVERT: D  368 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.6986 (p90)
REVERT: E   55 MET cc_start: 0.7726 (mmt) cc_final: 0.7265 (mmt)
REVERT: F  352 LYS cc_start: 0.8349 (mmtt) cc_final: 0.8066 (tppt)
  outliers start: 53
  outliers final: 38
  residues processed: 256
  average time/residue: 0.1354
  time to fit residues: 53.9927
Evaluate side-chains
  251 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 210
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  368 TYR
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  149 MET
Chi-restraints excluded: chain B residue  169 TYR
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  124 ASN
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  302 THR
Chi-restraints excluded: chain C residue  345 SER
Chi-restraints excluded: chain C residue  375 ASP
Chi-restraints excluded: chain C residue  384 VAL
Chi-restraints excluded: chain C residue  425 ASN
Chi-restraints excluded: chain D residue   87 ILE
Chi-restraints excluded: chain D residue  146 TYR
Chi-restraints excluded: chain D residue  253 VAL
Chi-restraints excluded: chain D residue  268 ILE
Chi-restraints excluded: chain D residue  368 TYR
Chi-restraints excluded: chain D residue  411 VAL
Chi-restraints excluded: chain D residue  420 VAL
Chi-restraints excluded: chain D residue  421 LEU
Chi-restraints excluded: chain D residue  470 THR
Chi-restraints excluded: chain D residue  493 VAL
Chi-restraints excluded: chain E residue   93 LEU
Chi-restraints excluded: chain E residue  133 ILE
Chi-restraints excluded: chain E residue  149 MET
Chi-restraints excluded: chain F residue  293 VAL
Chi-restraints excluded: chain F residue  302 THR
Chi-restraints excluded: chain F residue  345 SER
Chi-restraints excluded: chain F residue  384 VAL
Chi-restraints excluded: chain F residue  425 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 138 optimal weight:    4.9990
   chunk 163 optimal weight:    0.4980
   chunk 43 optimal weight:    0.5980
   chunk 62 optimal weight:    4.9990
   chunk 55 optimal weight:   10.0000
   chunk 24 optimal weight:    7.9990
   chunk 72 optimal weight:    0.0870
   chunk 81 optimal weight:    7.9990
   chunk 199 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 200 optimal weight:    4.9990
   overall best weight:    1.0362

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

Flipped N/Q/H residues before XYZ refinement:
** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 123 GLN
C 425 ASN
D 345 GLN
E 165 ASN
F 425 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.169342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.147639 restraints weight = 25250.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.147773 restraints weight = 25538.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.149176 restraints weight = 22530.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.149286 restraints weight = 16825.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.149378 restraints weight = 16537.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.121  17010  Z= 0.149
  Angle     :  1.443  83.950  23220  Z= 0.425
  Chirality :  0.060   1.436   2478
  Planarity :  0.005   0.061   2986
  Dihedral  :  9.403 106.404   2432
  Min Nonbonded Distance : 1.795

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 19.78 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.52 (0.19), residues: 2072
  helix:  0.61 (0.20), residues: 722
  sheet: -0.49 (0.40), residues: 184
  loop : -0.93 (0.19), residues: 1166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  41 
 TYR   0.051   0.002   TYR D  79 
 PHE   0.021   0.001   PHE C 423 
 TRP   0.016   0.001   TRP D 111 
 HIS   0.007   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (16972)
  covalent geometry    : angle       1.09233 (23202)
  hydrogen bonds       : bond        0.02801 (  513)
  hydrogen bonds       : angle       4.98458 ( 1431)
  metal coordination   : bond        0.00382 (    6)
  metal coordination   : angle      33.86508 (   18)
  Misc. bond           : bond        0.02515 (   32)

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

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

  4144 Ramachandran restraints generated.
    2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4144 Ramachandran restraints generated.
    2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 218
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 SER cc_start: 0.7606 (t) cc_final: 0.7241 (p)
REVERT: A   98 GLN cc_start: 0.7679 (pp30) cc_final: 0.7427 (pp30)
REVERT: A  109 TRP cc_start: 0.8034 (m100) cc_final: 0.7754 (m100)
REVERT: A  156 MET cc_start: 0.8344 (ttm) cc_final: 0.7817 (mtp)
REVERT: A  221 ASN cc_start: 0.8774 (t0) cc_final: 0.8411 (t0)
REVERT: A  329 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7594 (mmm)
REVERT: A  469 MET cc_start: 0.5912 (mtp) cc_final: 0.5616 (mtm)
REVERT: C  124 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8469 (t0)
REVERT: C  352 LYS cc_start: 0.8345 (mmtt) cc_final: 0.8060 (tppt)
REVERT: D   98 GLN cc_start: 0.7683 (pp30) cc_final: 0.7460 (pp30)
REVERT: D  221 ASN cc_start: 0.8780 (t0) cc_final: 0.8422 (t0)
REVERT: D  329 MET cc_start: 0.7359 (ttm) cc_final: 0.7003 (ttt)
REVERT: F  225 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8200 (pt)
REVERT: F  352 LYS cc_start: 0.8351 (mmtt) cc_final: 0.8066 (tppt)
  outliers start: 55
  outliers final: 42
  residues processed: 255
  average time/residue: 0.1280
  time to fit residues: 51.1026
Evaluate side-chains
  256 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 211
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  368 TYR
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  149 MET
Chi-restraints excluded: chain B residue  169 TYR
Chi-restraints excluded: chain C residue  124 ASN
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  302 THR
Chi-restraints excluded: chain C residue  345 SER
Chi-restraints excluded: chain C residue  375 ASP
Chi-restraints excluded: chain C residue  384 VAL
Chi-restraints excluded: chain C residue  425 ASN
Chi-restraints excluded: chain D residue   78 ASN
Chi-restraints excluded: chain D residue   87 ILE
Chi-restraints excluded: chain D residue  137 MET
Chi-restraints excluded: chain D residue  146 TYR
Chi-restraints excluded: chain D residue  253 VAL
Chi-restraints excluded: chain D residue  268 ILE
Chi-restraints excluded: chain D residue  411 VAL
Chi-restraints excluded: chain D residue  420 VAL
Chi-restraints excluded: chain D residue  421 LEU
Chi-restraints excluded: chain D residue  429 LEU
Chi-restraints excluded: chain D residue  470 THR
Chi-restraints excluded: chain D residue  493 VAL
Chi-restraints excluded: chain E residue   93 LEU
Chi-restraints excluded: chain E residue  122 ILE
Chi-restraints excluded: chain E residue  133 ILE
Chi-restraints excluded: chain E residue  149 MET
Chi-restraints excluded: chain F residue  225 ILE
Chi-restraints excluded: chain F residue  293 VAL
Chi-restraints excluded: chain F residue  302 THR
Chi-restraints excluded: chain F residue  345 SER
Chi-restraints excluded: chain F residue  384 VAL
Chi-restraints excluded: chain F residue  425 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 102 optimal weight:   10.0000
   chunk 63 optimal weight:    7.9990
   chunk 59 optimal weight:    3.9990
   chunk 163 optimal weight:    3.9990
   chunk 12 optimal weight:   10.0000
   chunk 151 optimal weight:    0.9990
   chunk 190 optimal weight:    9.9990
   chunk 181 optimal weight:    0.6980
   chunk 108 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 174 optimal weight:    3.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 118 HIS
** D 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.163751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.142423 restraints weight = 25391.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.142781 restraints weight = 27275.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.144114 restraints weight = 23140.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.144265 restraints weight = 18402.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.144530 restraints weight = 16544.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.2830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.185  17010  Z= 0.216
  Angle     :  1.528  84.060  23220  Z= 0.453
  Chirality :  0.062   1.476   2478
  Planarity :  0.006   0.065   2986
  Dihedral  :  9.532 111.117   2432
  Min Nonbonded Distance : 1.801

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 19.37 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.71 (0.19), residues: 2072
  helix:  0.51 (0.20), residues: 722
  sheet: -0.58 (0.40), residues: 184
  loop : -1.09 (0.18), residues: 1166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 396 
 TYR   0.047   0.002   TYR D  79 
 PHE   0.018   0.002   PHE C 306 
 TRP   0.015   0.002   TRP D 497 
 HIS   0.006   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 (16972)
  covalent geometry    : angle       1.13928 (23202)
  hydrogen bonds       : bond        0.03211 (  513)
  hydrogen bonds       : angle       5.15674 ( 1431)
  metal coordination   : bond        0.00400 (    6)
  metal coordination   : angle      36.56531 (   18)
  Misc. bond           : bond        0.04504 (   32)

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

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

  4144 Ramachandran restraints generated.
    2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4144 Ramachandran restraints generated.
    2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 205
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 SER cc_start: 0.7756 (t) cc_final: 0.7192 (p)
REVERT: A   98 GLN cc_start: 0.7791 (pp30) cc_final: 0.7487 (pp30)
REVERT: A  156 MET cc_start: 0.8396 (ttm) cc_final: 0.8002 (mtp)
REVERT: A  221 ASN cc_start: 0.8868 (t0) cc_final: 0.8506 (t0)
REVERT: A  329 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7666 (mmm)
REVERT: C  124 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8397 (t0)
REVERT: C  352 LYS cc_start: 0.8568 (mmtt) cc_final: 0.8206 (tppt)
REVERT: D   98 GLN cc_start: 0.7798 (pp30) cc_final: 0.7530 (pp30)
REVERT: D  156 MET cc_start: 0.8320 (ttm) cc_final: 0.8021 (mtp)
REVERT: D  221 ASN cc_start: 0.8871 (t0) cc_final: 0.8492 (t0)
REVERT: D  329 MET cc_start: 0.7444 (ttm) cc_final: 0.7051 (ttt)
REVERT: F  124 ASN cc_start: 0.8779 (OUTLIER) cc_final: 0.8378 (t0)
  outliers start: 60
  outliers final: 46
  residues processed: 248
  average time/residue: 0.1245
  time to fit residues: 49.0172
Evaluate side-chains
  252 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 203
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  368 TYR
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  149 MET
Chi-restraints excluded: chain B residue  159 ILE
Chi-restraints excluded: chain B residue  169 TYR
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  124 ASN
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  302 THR
Chi-restraints excluded: chain C residue  345 SER
Chi-restraints excluded: chain C residue  375 ASP
Chi-restraints excluded: chain C residue  384 VAL
Chi-restraints excluded: chain C residue  393 ILE
Chi-restraints excluded: chain D residue   60 SER
Chi-restraints excluded: chain D residue   87 ILE
Chi-restraints excluded: chain D residue  146 TYR
Chi-restraints excluded: chain D residue  253 VAL
Chi-restraints excluded: chain D residue  268 ILE
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  337 ILE
Chi-restraints excluded: chain D residue  368 TYR
Chi-restraints excluded: chain D residue  411 VAL
Chi-restraints excluded: chain D residue  420 VAL
Chi-restraints excluded: chain D residue  429 LEU
Chi-restraints excluded: chain D residue  470 THR
Chi-restraints excluded: chain D residue  493 VAL
Chi-restraints excluded: chain E residue   93 LEU
Chi-restraints excluded: chain E residue  122 ILE
Chi-restraints excluded: chain E residue  133 ILE
Chi-restraints excluded: chain E residue  149 MET
Chi-restraints excluded: chain F residue  103 LEU
Chi-restraints excluded: chain F residue  124 ASN
Chi-restraints excluded: chain F residue  293 VAL
Chi-restraints excluded: chain F residue  302 THR
Chi-restraints excluded: chain F residue  345 SER
Chi-restraints excluded: chain F residue  384 VAL
Chi-restraints excluded: chain F residue  393 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 104 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 25 optimal weight:   10.0000
   chunk 46 optimal weight:    0.7980
   chunk 193 optimal weight:    2.9990
   chunk 160 optimal weight:   10.0000
   chunk 90 optimal weight:    4.9990
   chunk 132 optimal weight:    0.0970
   chunk 67 optimal weight:    2.9990
   chunk 99 optimal weight:   10.0000
   chunk 184 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 425 ASN
** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 425 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.169132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.147704 restraints weight = 25172.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.147619 restraints weight = 28363.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.149333 restraints weight = 23585.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.149550 restraints weight = 18280.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.149782 restraints weight = 17531.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.117  17010  Z= 0.145
  Angle     :  1.446  84.176  23220  Z= 0.426
  Chirality :  0.060   1.412   2478
  Planarity :  0.005   0.063   2986
  Dihedral  :  9.370 108.841   2432
  Min Nonbonded Distance : 1.797

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 20.42 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.19), residues: 2072
  helix:  0.60 (0.20), residues: 722
  sheet: -0.61 (0.40), residues: 184
  loop : -0.97 (0.19), residues: 1166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 205 
 TYR   0.042   0.002   TYR D  79 
 PHE   0.017   0.001   PHE F 210 
 TRP   0.018   0.001   TRP D 111 
 HIS   0.006   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (16972)
  covalent geometry    : angle       1.09791 (23202)
  hydrogen bonds       : bond        0.02793 (  513)
  hydrogen bonds       : angle       4.96586 ( 1431)
  metal coordination   : bond        0.00420 (    6)
  metal coordination   : angle      33.80715 (   18)
  Misc. bond           : bond        0.02547 (   32)

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

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

  4144 Ramachandran restraints generated.
    2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4144 Ramachandran restraints generated.
    2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 217
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 SER cc_start: 0.7620 (t) cc_final: 0.7196 (p)
REVERT: A   98 GLN cc_start: 0.7662 (pp30) cc_final: 0.7393 (pp30)
REVERT: A  156 MET cc_start: 0.8394 (ttm) cc_final: 0.8005 (mtp)
REVERT: A  221 ASN cc_start: 0.8770 (t0) cc_final: 0.8389 (t0)
REVERT: A  329 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7465 (mmm)
REVERT: B   94 ARG cc_start: 0.5001 (mtt90) cc_final: 0.4580 (mtt90)
REVERT: C  124 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8465 (t0)
REVERT: C  352 LYS cc_start: 0.8366 (mmtt) cc_final: 0.8067 (tppt)
REVERT: C  405 GLN cc_start: 0.8391 (tm-30) cc_final: 0.7768 (tt0)
REVERT: D   98 GLN cc_start: 0.7639 (pp30) cc_final: 0.7413 (pp30)
REVERT: D  156 MET cc_start: 0.8292 (ttm) cc_final: 0.7970 (mtp)
REVERT: D  221 ASN cc_start: 0.8801 (t0) cc_final: 0.8413 (t0)
REVERT: D  329 MET cc_start: 0.7367 (ttm) cc_final: 0.6934 (ttt)
REVERT: F  352 LYS cc_start: 0.8361 (mmtt) cc_final: 0.8056 (tppt)
  outliers start: 44
  outliers final: 39
  residues processed: 244
  average time/residue: 0.1352
  time to fit residues: 51.3450
Evaluate side-chains
  248 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 207
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ILE
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  368 TYR
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  133 ILE
Chi-restraints excluded: chain B residue  149 MET
Chi-restraints excluded: chain B residue  169 TYR
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  124 ASN
Chi-restraints excluded: chain C residue  293 VAL
Chi-restraints excluded: chain C residue  302 THR
Chi-restraints excluded: chain C residue  345 SER
Chi-restraints excluded: chain C residue  375 ASP
Chi-restraints excluded: chain C residue  384 VAL
Chi-restraints excluded: chain C residue  425 ASN
Chi-restraints excluded: chain D residue   78 ASN
Chi-restraints excluded: chain D residue   87 ILE
Chi-restraints excluded: chain D residue  146 TYR
Chi-restraints excluded: chain D residue  253 VAL
Chi-restraints excluded: chain D residue  268 ILE
Chi-restraints excluded: chain D residue  368 TYR
Chi-restraints excluded: chain D residue  411 VAL
Chi-restraints excluded: chain D residue  429 LEU
Chi-restraints excluded: chain D residue  470 THR
Chi-restraints excluded: chain D residue  493 VAL
Chi-restraints excluded: chain E residue   93 LEU
Chi-restraints excluded: chain E residue  133 ILE
Chi-restraints excluded: chain E residue  149 MET
Chi-restraints excluded: chain F residue  293 VAL
Chi-restraints excluded: chain F residue  302 THR
Chi-restraints excluded: chain F residue  345 SER
Chi-restraints excluded: chain F residue  384 VAL
Chi-restraints excluded: chain F residue  425 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 141 optimal weight:    0.6980
   chunk 26 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 135 optimal weight:    0.0870
   chunk 132 optimal weight:    0.5980
   chunk 187 optimal weight:    5.9990
   chunk 108 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 29 optimal weight:    8.9990
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.8762

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.169218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.147762 restraints weight = 25281.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.147925 restraints weight = 26857.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.149410 restraints weight = 23516.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.149582 restraints weight = 17759.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.149951 restraints weight = 15956.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.2869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.118  17010  Z= 0.146
  Angle     :  1.443  83.943  23220  Z= 0.426
  Chirality :  0.060   1.429   2478
  Planarity :  0.005   0.062   2986
  Dihedral  :  9.280 107.434   2432
  Min Nonbonded Distance : 1.795

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 20.48 %
    Favored  : 76.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.10 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.55 (0.19), residues: 2072
  helix:  0.61 (0.20), residues: 724
  sheet: -0.60 (0.40), residues: 184
  loop : -0.95 (0.19), residues: 1164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 190 
 TYR   0.039   0.002   TYR D  79 
 PHE   0.017   0.001   PHE C 210 
 TRP   0.018   0.001   TRP D 111 
 HIS   0.006   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (16972)
  covalent geometry    : angle       1.09592 (23202)
  hydrogen bonds       : bond        0.02793 (  513)
  hydrogen bonds       : angle       4.92667 ( 1431)
  metal coordination   : bond        0.00388 (    6)
  metal coordination   : angle      33.75025 (   18)
  Misc. bond           : bond        0.02539 (   32)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2359.97 seconds
wall clock time: 42 minutes 7.98 seconds (2527.98 seconds total)