Starting phenix.real_space_refine
on Sat Dec 28 07:31:38 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d6a_27221/12_2024/8d6a_27221.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d6a_27221/12_2024/8d6a_27221.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d6a_27221/12_2024/8d6a_27221.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d6a_27221/12_2024/8d6a_27221.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d6a_27221/12_2024/8d6a_27221.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d6a_27221/12_2024/8d6a_27221.cif"
  }
  resolution = 3.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    5043      2.51       5
     N    1321      2.21       5
     O    1516      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 7912
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "D"
      Number of atoms: 1310
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 169, 1310
          Classifications: {'peptide': 169}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 160}
    Chain: "A"
      Number of atoms: 3167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 392, 3167
          Classifications: {'peptide': 392}
          Link IDs: {'CIS': 1, 'PTRANS': 25, 'TRANS': 365}
    Chain: "B"
      Number of atoms: 3225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 402, 3225
          Classifications: {'peptide': 402}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 381}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "H"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 6.33, per 1000 atoms: 0.80
  Number of scatterers: 7912
  At special positions: 0
  Unit cell: (104.06, 141.04, 160.82, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1516      8.00
     N    1321      7.00
     C    5043      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  34 " - pdb=" SG  CYS D 156 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  40 " - pdb=" SG  CYS D 153 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  82 " - pdb=" SG  CYS D 185 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 134 " - pdb=" SG  CYS A 144 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 172 " - pdb=" SG  CYS A 182 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 458 " - pdb=" SG  CYS A 466 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 213 " - pdb=" SG  CYS B 270 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 341 " - pdb=" SG  CYS B 351 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 466 " - pdb=" SG  CYS B 511 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
    NAG-ASN
      " NAG A 701 " - " ASN A 131 "
      " NAG A 702 " - " ASN A 390 "
      " NAG A 703 " - " ASN A 157 "
      " NAG A 704 " - " ASN A 383 "
      " NAG A 705 " - " ASN A 379 "
      " NAG C   1 " - " ASN A 227 "
      " NAG E   1 " - " ASN B 407 "
      " NAG F   1 " - " ASN B 426 "
      " NAG G   1 " - " ASN B 303 "
      " NAG H   1 " - " ASN B 243 "
  Time building additional restraints: 2.05
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1844

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 21 sheets defined
      13.8% alpha, 25.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'D' and resid 43 through 70
    Processing helix  chain 'D' and resid 72 through 77
      removed outlier: 4.404A  pdb=" N   ASN D  76 " --> pdb=" O   GLU D  72 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ASN D  77 " --> pdb=" O   PRO D  73 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 72 through 77'
    Processing helix  chain 'D' and resid 77 through 82
    Processing helix  chain 'D' and resid 97 through 127
    Processing helix  chain 'D' and resid 131 through 159
    Processing helix  chain 'D' and resid 176 through 202
      removed outlier: 3.792A  pdb=" N   GLN D 200 " --> pdb=" O   ALA D 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 252
      removed outlier: 3.956A  pdb=" N   SER A 251 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 143 through 144
      removed outlier: 9.418A  pdb=" N   LYS A 221 " --> pdb=" O   CYS A 134 " (cutoff:3.500A)
      removed outlier: 7.984A  pdb=" N   VAL A 136 " --> pdb=" O   LYS A 221 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 160
    Processing sheet with id=AA3, first strand: chain 'A' and resid 194 through 196
      removed outlier: 3.733A  pdb=" N   PHE A 214 " --> pdb=" O   ILE A 194 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL A 196 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ILE A 212 " --> pdb=" O   VAL A 196 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 199 through 200
      removed outlier: 3.561A  pdb=" N   VAL A 207 " --> pdb=" O   ALA A 200 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 226 through 232
      removed outlier: 6.149A  pdb=" N   ASN A 227 " --> pdb=" O   THR A 245 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   THR A 245 " --> pdb=" O   ASN A 227 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ILE A 231 " --> pdb=" O   LYS A 241 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 270 through 271
    Processing sheet with id=AA7, first strand: chain 'A' and resid 332 through 336
      removed outlier: 3.790A  pdb=" N   ARG A 345 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   VAL A 389 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   LEU A 349 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LEU A 387 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 378 through 380
      removed outlier: 3.573A  pdb=" N   LEU A 370 " --> pdb=" O   GLN A 378 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ASP A 365 " --> pdb=" O   ARG A 403 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   TYR A 396 " --> pdb=" O   ILE A 416 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ILE A 416 " --> pdb=" O   TYR A 396 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 431 through 433
      removed outlier: 3.956A  pdb=" N   PHE A 433 " --> pdb=" O   TRP A 440 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   TRP A 440 " --> pdb=" O   PHE A 433 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 469 through 473
      removed outlier: 3.556A  pdb=" N   GLN A 471 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU A 455 " --> pdb=" O   GLN A 471 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ILE A 454 " --> pdb=" O   THR A 497 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   THR A 497 " --> pdb=" O   ILE A 454 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLY A 503 " --> pdb=" O   TYR A 500 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 469 through 473
      removed outlier: 3.556A  pdb=" N   GLN A 471 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU A 455 " --> pdb=" O   GLN A 471 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ILE A 454 " --> pdb=" O   THR A 497 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   THR A 497 " --> pdb=" O   ILE A 454 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   TYR A 492 " --> pdb=" O   ALA A 512 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ALA A 512 " --> pdb=" O   TYR A 492 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   GLU A 508 " --> pdb=" O   VAL A 496 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 133 through 134
    Processing sheet with id=AB4, first strand: chain 'B' and resid 143 through 147
      removed outlier: 3.738A  pdb=" N   ASN B 143 " --> pdb=" O   LYS B 156 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 185 through 192
      removed outlier: 3.837A  pdb=" N   ASN B 169 " --> pdb=" O   ASP B 225 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLU B 173 " --> pdb=" O   ARG B 221 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ARG B 221 " --> pdb=" O   GLU B 173 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   LYS B 175 " --> pdb=" O   GLU B 219 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   GLU B 219 " --> pdb=" O   LYS B 175 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   HIS B 216 " --> pdb=" O   ILE B 244 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE B 244 " --> pdb=" O   HIS B 216 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   VAL B 218 " --> pdb=" O   LYS B 242 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LYS B 242 " --> pdb=" O   VAL B 218 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 254 through 255
      removed outlier: 3.658A  pdb=" N   ILE B 267 " --> pdb=" O   ILE B 301 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE B 301 " --> pdb=" O   ILE B 267 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   VAL B 297 " --> pdb=" O   CYS B 271 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 259 through 262
      removed outlier: 6.299A  pdb=" N   LYS B 259 " --> pdb=" O   PHE B 328 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   GLY B 330 " --> pdb=" O   LYS B 259 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   ILE B 261 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   PHE B 323 " --> pdb=" O   PHE B 316 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   THR B 312 " --> pdb=" O   ILE B 327 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   SER B 279 " --> pdb=" O   THR B 317 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 337 through 340
      removed outlier: 3.657A  pdb=" N   GLN B 337 " --> pdb=" O   ASN B 354 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ASN B 354 " --> pdb=" O   GLN B 337 " (cutoff:3.500A)
      removed outlier: 4.724A  pdb=" N   LEU B 339 " --> pdb=" O   SER B 352 " (cutoff:3.500A)
      removed outlier: 7.340A  pdb=" N   SER B 352 " --> pdb=" O   LEU B 339 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'B' and resid 348 through 350
    Processing sheet with id=AC1, first strand: chain 'B' and resid 379 through 381
      removed outlier: 3.627A  pdb=" N   TYR B 406 " --> pdb=" O   VAL B 425 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER B 419 " --> pdb=" O   ALA B 412 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 437 through 440
      removed outlier: 3.761A  pdb=" N   HIS B 454 " --> pdb=" O   THR B 437 " (cutoff:3.500A)
      removed outlier: 4.804A  pdb=" N   PHE B 439 " --> pdb=" O   SER B 452 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   SER B 452 " --> pdb=" O   PHE B 439 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 477 through 481
      removed outlier: 3.823A  pdb=" N   ARG B 480 " --> pdb=" O   ILE B 468 " (cutoff:3.500A)

    238 hydrogen bonds defined for protein.
    648 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: 2.25

  Time building geometry restraints manager: 2.39 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2485
        1.35 -     1.47: 2021
        1.47 -     1.59: 3565
        1.59 -     1.71: 0
        1.71 -     1.83: 40
  Bond restraints: 8111
  Sorted by residual:
  bond pdb=" C1  NAG E   1 "
       pdb=" O5  NAG E   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.63e+00
  bond pdb=" C1  NAG H   2 "
       pdb=" O5  NAG H   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.20e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.19e+00
  bond pdb=" C1  NAG F   1 "
       pdb=" O5  NAG F   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.15e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.10e+00
  ... (remaining 8106 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 10742
        1.55 -     3.10: 270
        3.10 -     4.64: 30
        4.64 -     6.19: 5
        6.19 -     7.74: 2
  Bond angle restraints: 11049
  Sorted by residual:
  angle pdb=" C   GLU A 151 "
        pdb=" N   THR A 152 "
        pdb=" CA  THR A 152 "
      ideal   model   delta    sigma   weight residual
     121.54  128.25   -6.71 1.91e+00 2.74e-01 1.24e+01
  angle pdb=" C   LYS A 130 "
        pdb=" N   ASN A 131 "
        pdb=" CA  ASN A 131 "
      ideal   model   delta    sigma   weight residual
     121.54  127.26   -5.72 1.91e+00 2.74e-01 8.96e+00
  angle pdb=" C   ASN A 131 "
        pdb=" N   LEU A 132 "
        pdb=" CA  LEU A 132 "
      ideal   model   delta    sigma   weight residual
     121.54  126.30   -4.76 1.91e+00 2.74e-01 6.21e+00
  angle pdb=" CA  TYR D  67 "
        pdb=" CB  TYR D  67 "
        pdb=" CG  TYR D  67 "
      ideal   model   delta    sigma   weight residual
     113.90  118.23   -4.33 1.80e+00 3.09e-01 5.78e+00
  angle pdb=" N   THR A 166 "
        pdb=" CA  THR A 166 "
        pdb=" C   THR A 166 "
      ideal   model   delta    sigma   weight residual
     113.18  110.18    3.00 1.33e+00 5.65e-01 5.10e+00
  ... (remaining 11044 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.50: 4729
       21.50 -    43.00: 236
       43.00 -    64.50: 55
       64.50 -    86.00: 13
       86.00 -   107.50: 34
  Dihedral angle restraints: 5067
    sinusoidal: 2227
      harmonic: 2840
  Sorted by residual:
  dihedral pdb=" CB  CYS A 172 "
           pdb=" SG  CYS A 172 "
           pdb=" SG  CYS A 182 "
           pdb=" CB  CYS A 182 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  141.21  -48.21     1      1.00e+01 1.00e-02 3.20e+01
  dihedral pdb=" CA  ASN A 131 "
           pdb=" C   ASN A 131 "
           pdb=" N   LEU A 132 "
           pdb=" CA  LEU A 132 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.57   24.43     0      5.00e+00 4.00e-02 2.39e+01
  dihedral pdb=" CA  THR B 447 "
           pdb=" C   THR B 447 "
           pdb=" N   ALA B 448 "
           pdb=" CA  ALA B 448 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.68  -24.32     0      5.00e+00 4.00e-02 2.37e+01
  ... (remaining 5064 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1116
       0.065 -    0.130: 168
       0.130 -    0.195: 6
       0.195 -    0.260: 0
       0.260 -    0.324: 2
  Chirality restraints: 1292
  Sorted by residual:
  chirality pdb=" C1  NAG A 702 "
            pdb=" ND2 ASN A 390 "
            pdb=" C2  NAG A 702 "
            pdb=" O5  NAG A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.08   -0.32 2.00e-01 2.50e+01 2.63e+00
  chirality pdb=" C1  NAG A 704 "
            pdb=" ND2 ASN A 383 "
            pdb=" C2  NAG A 704 "
            pdb=" O5  NAG A 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.10   -0.30 2.00e-01 2.50e+01 2.26e+00
  chirality pdb=" C1  NAG A 701 "
            pdb=" ND2 ASN A 131 "
            pdb=" C2  NAG A 701 "
            pdb=" O5  NAG A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-01 2.50e+01 8.92e-01
  ... (remaining 1289 not shown)

  Planarity restraints: 1384
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 500 "   -0.041 5.00e-02 4.00e+02   6.28e-02 6.32e+00
        pdb=" N   PRO B 501 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO B 501 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 501 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 325 "   -0.025 5.00e-02 4.00e+02   3.75e-02 2.25e+00
        pdb=" N   PRO A 326 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 326 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 326 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 445 "   -0.023 5.00e-02 4.00e+02   3.42e-02 1.87e+00
        pdb=" N   PRO A 446 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 446 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 446 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1381 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1725
        2.79 -     3.32: 7108
        3.32 -     3.84: 12077
        3.84 -     4.37: 13247
        4.37 -     4.90: 23412
  Nonbonded interactions: 57569
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 454 "
            pdb=" OG1 THR A 497 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   HIS A 425 "
            pdb=" OH  TYR A 500 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O   SER A 133 "
            pdb=" N   GLU A 145 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" O   ILE D  64 "
            pdb=" OG1 THR D  68 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" O   SER B 473 "
            pdb=" OG  SER B 473 "
     model   vdw
     2.302 3.040
  ... (remaining 57564 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

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=0.00 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:             3.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     22.370
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7128
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      :  0.003   0.032   8111  Z= 0.180
  Angle     :  0.560   7.738  11049  Z= 0.288
  Chirality :  0.044   0.324   1292
  Planarity :  0.004   0.063   1374
  Dihedral  : 16.683 107.504   3196
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.01 (0.24), residues: 957
  helix:  1.02 (0.44), residues: 124
  sheet: -1.81 (0.27), residues: 308
  loop : -2.98 (0.22), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP B 517 
 HIS   0.004   0.000   HIS B 434 
 PHE   0.005   0.000   PHE A 332 
 TYR   0.017   0.001   TYR D  67 
 ARG   0.001   0.000   ARG A 372 

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

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

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 ASP cc_start: 0.8500 (p0) cc_final: 0.8173 (p0)
REVERT: B  442 LYS cc_start: 0.7751 (tppt) cc_final: 0.7531 (tppt)
REVERT: B  503 THR cc_start: 0.6822 (m) cc_final: 0.6186 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.2338
  time to fit residues: 47.0229
Evaluate side-chains
  90 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 72 optimal weight:    0.0170
   chunk 39 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    0.3980
   chunk 38 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 28 optimal weight:    0.1980
   chunk 45 optimal weight:    7.9990
   chunk 55 optimal weight:    0.7980
   chunk 86 optimal weight:    0.5980
   overall best weight:    0.4018

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

Flipped N/Q/H residues before XYZ refinement:
D  47 GLN
D  51 GLN
D  54 GLN
D  76 ASN
D 150 ASN
D 193 GLN
A 258 ASN
A 342 GLN
A 360 ASN
A 404 ASN
A 425 HIS
B 158 ASN
B 190 HIS
B 479 GLN
B 527 GLN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8111  Z= 0.176
  Angle     :  0.627   7.364  11049  Z= 0.310
  Chirality :  0.046   0.297   1292
  Planarity :  0.005   0.059   1374
  Dihedral  : 14.224  88.777   1346
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.46 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  :  9.17 %
    Favored  : 88.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.38 (0.25), residues: 957
  helix:  2.03 (0.45), residues: 125
  sheet: -1.51 (0.26), residues: 320
  loop : -2.65 (0.23), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP B 172 
 HIS   0.003   0.001   HIS B 434 
 PHE   0.012   0.001   PHE A 297 
 TYR   0.025   0.001   TYR A 396 
 ARG   0.004   0.000   ARG D 121 

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

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

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 ASP cc_start: 0.8468 (p0) cc_final: 0.8154 (p0)
  outliers start: 22
  outliers final: 7
  residues processed: 98
  average time/residue: 0.1768
  time to fit residues: 24.8352
Evaluate side-chains
  81 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  164 TRP
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  500 TYR
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  282 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0370
   chunk 71 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0000
   chunk 93 optimal weight:    0.8980
   chunk 76 optimal weight:    0.7980
   chunk 85 optimal weight:    0.0040
   chunk 29 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.3074

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

Flipped N/Q/H residues before XYZ refinement:
D  70 GLN
A 167 HIS
A 258 ASN
A 404 ASN
A 478 HIS
B 190 HIS
B 434 HIS
** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8111  Z= 0.148
  Angle     :  0.599   8.996  11049  Z= 0.294
  Chirality :  0.045   0.359   1292
  Planarity :  0.004   0.058   1374
  Dihedral  : 10.255  77.704   1346
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.88 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.25), residues: 957
  helix:  2.71 (0.45), residues: 119
  sheet: -1.28 (0.26), residues: 320
  loop : -2.37 (0.24), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP B 172 
 HIS   0.003   0.001   HIS A 167 
 PHE   0.010   0.001   PHE A 297 
 TYR   0.022   0.001   TYR A 396 
 ARG   0.006   0.000   ARG D 121 

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

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

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 LEU cc_start: 0.6345 (mt) cc_final: 0.5540 (pp)
REVERT: A  177 ASP cc_start: 0.8506 (p0) cc_final: 0.8168 (p0)
REVERT: A  438 MET cc_start: 0.6475 (pmm) cc_final: 0.6268 (pmm)
  outliers start: 17
  outliers final: 12
  residues processed: 99
  average time/residue: 0.1929
  time to fit residues: 26.6366
Evaluate side-chains
  95 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain D residue  119 ILE
Chi-restraints excluded: chain A residue  164 TRP
Chi-restraints excluded: chain A residue  167 HIS
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  404 ASN
Chi-restraints excluded: chain A residue  500 TYR
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  503 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 85 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0000
   chunk 9 optimal weight:    0.0470
   chunk 41 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 86 optimal weight:    0.0670
   chunk 91 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.3422

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

Flipped N/Q/H residues before XYZ refinement:
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 404 ASN
** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS
B 251 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.2547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8111  Z= 0.146
  Angle     :  0.577   7.555  11049  Z= 0.287
  Chirality :  0.044   0.349   1292
  Planarity :  0.004   0.057   1374
  Dihedral  :  9.055  72.402   1346
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 14.79 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.25), residues: 957
  helix:  2.88 (0.45), residues: 119
  sheet: -1.14 (0.26), residues: 317
  loop : -2.31 (0.24), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP B 172 
 HIS   0.004   0.001   HIS A 167 
 PHE   0.010   0.001   PHE A 297 
 TYR   0.011   0.001   TYR A 492 
 ARG   0.003   0.000   ARG A 403 

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

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

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  119 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8967 (mt)
REVERT: A  132 LEU cc_start: 0.6295 (mt) cc_final: 0.5582 (pp)
REVERT: A  177 ASP cc_start: 0.8490 (p0) cc_final: 0.8165 (p0)
REVERT: A  438 MET cc_start: 0.6397 (pmm) cc_final: 0.6169 (pmm)
REVERT: B  442 LYS cc_start: 0.7579 (mmmt) cc_final: 0.7258 (mmmt)
  outliers start: 22
  outliers final: 14
  residues processed: 99
  average time/residue: 0.1905
  time to fit residues: 26.4041
Evaluate side-chains
  94 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain D residue  119 ILE
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  164 TRP
Chi-restraints excluded: chain A residue  167 HIS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  404 ASN
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  500 TYR
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  503 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   chunk 37 optimal weight:    8.9990
   chunk 78 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 46 optimal weight:    9.9990
   chunk 82 optimal weight:    0.0010
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.9590

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

Flipped N/Q/H residues before XYZ refinement:
A 153 HIS
A 167 HIS
A 258 ASN
** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS
** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8111  Z= 0.219
  Angle     :  0.627  12.626  11049  Z= 0.309
  Chirality :  0.045   0.339   1292
  Planarity :  0.004   0.063   1374
  Dihedral  :  8.411  67.076   1346
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.37 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.26), residues: 957
  helix:  2.59 (0.46), residues: 122
  sheet: -1.04 (0.26), residues: 330
  loop : -2.31 (0.25), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 172 
 HIS   0.005   0.001   HIS A 167 
 PHE   0.011   0.001   PHE A 297 
 TYR   0.012   0.001   TYR B 406 
 ARG   0.004   0.001   ARG A 176 

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

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

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   62 LEU cc_start: 0.9056 (tp) cc_final: 0.8798 (tp)
REVERT: A  177 ASP cc_start: 0.8483 (p0) cc_final: 0.8101 (p0)
REVERT: B  453 TRP cc_start: 0.6142 (p90) cc_final: 0.5838 (p90)
REVERT: B  469 GLU cc_start: 0.4468 (OUTLIER) cc_final: 0.4142 (pt0)
  outliers start: 23
  outliers final: 17
  residues processed: 99
  average time/residue: 0.2000
  time to fit residues: 27.6984
Evaluate side-chains
  96 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  164 TRP
Chi-restraints excluded: chain A residue  167 HIS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  350 ILE
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain B residue  513 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 30 optimal weight:    0.2980
   chunk 82 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 91 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0370
   chunk 42 optimal weight:    0.0370
   chunk 7 optimal weight:    0.5980
   chunk 48 optimal weight:    3.9990
   chunk 88 optimal weight:    0.5980
   overall best weight:    0.3136

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

Flipped N/Q/H residues before XYZ refinement:
A 167 HIS
** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS
B 251 GLN
** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.3240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8111  Z= 0.160
  Angle     :  0.601   9.429  11049  Z= 0.296
  Chirality :  0.045   0.331   1292
  Planarity :  0.004   0.057   1374
  Dihedral  :  7.986  63.503   1346
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 15.60 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.26), residues: 957
  helix:  2.35 (0.46), residues: 128
  sheet: -0.94 (0.27), residues: 335
  loop : -2.13 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 172 
 HIS   0.011   0.001   HIS A 167 
 PHE   0.009   0.001   PHE A 297 
 TYR   0.026   0.001   TYR A 366 
 ARG   0.007   0.000   ARG D 154 

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

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

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 79
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   62 LEU cc_start: 0.8989 (tp) cc_final: 0.8743 (tp)
REVERT: D  119 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.9054 (mt)
REVERT: A  177 ASP cc_start: 0.8492 (p0) cc_final: 0.8097 (p0)
REVERT: A  438 MET cc_start: 0.6366 (pmm) cc_final: 0.6083 (pmm)
REVERT: A  452 LYS cc_start: 0.6917 (mmmm) cc_final: 0.6573 (mmtt)
REVERT: B  453 TRP cc_start: 0.6194 (p90) cc_final: 0.5927 (p90)
REVERT: B  469 GLU cc_start: 0.4458 (OUTLIER) cc_final: 0.3817 (pt0)
  outliers start: 26
  outliers final: 16
  residues processed: 98
  average time/residue: 0.1853
  time to fit residues: 25.8715
Evaluate side-chains
  93 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   40 CYS
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain D residue  119 ILE
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  164 TRP
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  500 TYR
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain B residue  513 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 52 optimal weight:    0.1980
   chunk 67 optimal weight:    3.9990
   chunk 77 optimal weight:    0.0670
   chunk 51 optimal weight:    0.6980
   chunk 91 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 55 optimal weight:    0.2980
   chunk 42 optimal weight:    7.9990
   chunk 56 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0030
   overall best weight:    0.2528

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

Flipped N/Q/H residues before XYZ refinement:
A 258 ASN
A 478 HIS
B 190 HIS
** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8111  Z= 0.147
  Angle     :  0.606  18.648  11049  Z= 0.289
  Chirality :  0.044   0.327   1292
  Planarity :  0.004   0.055   1374
  Dihedral  :  7.539  59.418   1346
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 15.83 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.27), residues: 957
  helix:  2.37 (0.47), residues: 128
  sheet: -0.82 (0.27), residues: 335
  loop : -2.06 (0.27), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 172 
 HIS   0.003   0.001   HIS B 216 
 PHE   0.008   0.001   PHE A 297 
 TYR   0.023   0.001   TYR A 366 
 ARG   0.003   0.000   ARG B 178 

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

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

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 77
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  119 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.9001 (mt)
REVERT: A  132 LEU cc_start: 0.6593 (mt) cc_final: 0.5842 (pp)
REVERT: A  177 ASP cc_start: 0.8586 (p0) cc_final: 0.8240 (p0)
REVERT: A  438 MET cc_start: 0.6339 (pmm) cc_final: 0.6060 (pmm)
REVERT: A  452 LYS cc_start: 0.6928 (mmmm) cc_final: 0.6667 (mmtt)
REVERT: B  469 GLU cc_start: 0.4360 (OUTLIER) cc_final: 0.3752 (pt0)
  outliers start: 28
  outliers final: 21
  residues processed: 96
  average time/residue: 0.1967
  time to fit residues: 26.2070
Evaluate side-chains
  97 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 74
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   40 CYS
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain D residue  119 ILE
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  164 TRP
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  421 PHE
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  478 HIS
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  500 TYR
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain B residue  513 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 58 optimal weight:    7.9990
   chunk 62 optimal weight:    0.0570
   chunk 45 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.9702

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

Flipped N/Q/H residues before XYZ refinement:
B 190 HIS
** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.3676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8111  Z= 0.219
  Angle     :  0.637  18.503  11049  Z= 0.309
  Chirality :  0.045   0.328   1292
  Planarity :  0.004   0.055   1374
  Dihedral  :  7.398  56.419   1346
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.99 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 16.28 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.56 (0.27), residues: 957
  helix:  2.07 (0.47), residues: 131
  sheet: -0.81 (0.27), residues: 335
  loop : -2.13 (0.27), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 172 
 HIS   0.013   0.001   HIS A 478 
 PHE   0.009   0.001   PHE A 297 
 TYR   0.015   0.001   TYR B 406 
 ARG   0.012   0.001   ARG A 176 

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

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

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 73
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 ASP cc_start: 0.8647 (p0) cc_final: 0.8294 (p0)
REVERT: A  452 LYS cc_start: 0.7033 (mmmm) cc_final: 0.6707 (mmtt)
REVERT: B  469 GLU cc_start: 0.4566 (OUTLIER) cc_final: 0.3952 (pt0)
  outliers start: 23
  outliers final: 19
  residues processed: 88
  average time/residue: 0.1832
  time to fit residues: 23.2332
Evaluate side-chains
  90 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   40 CYS
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  164 TRP
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  478 HIS
Chi-restraints excluded: chain A residue  500 TYR
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain B residue  513 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 87 optimal weight:    0.0970
   chunk 51 optimal weight:    0.3980
   chunk 37 optimal weight:    0.0670
   chunk 67 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   chunk 56 optimal weight:    0.3980
   chunk 90 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0050
   overall best weight:    0.1930

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

Flipped N/Q/H residues before XYZ refinement:
A 258 ASN
** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS
** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.3669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.067   8111  Z= 0.151
  Angle     :  0.623  13.106  11049  Z= 0.300
  Chirality :  0.045   0.328   1292
  Planarity :  0.004   0.053   1374
  Dihedral  :  6.898  53.131   1346
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.78 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 16.86 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.40 (0.27), residues: 957
  helix:  2.50 (0.47), residues: 125
  sheet: -0.69 (0.27), residues: 335
  loop : -2.08 (0.27), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 172 
 HIS   0.007   0.001   HIS A 478 
 PHE   0.007   0.001   PHE A 297 
 TYR   0.010   0.001   TYR A 492 
 ARG   0.006   0.000   ARG A 176 

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

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

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 ASP cc_start: 0.8669 (p0) cc_final: 0.8252 (p0)
REVERT: A  438 MET cc_start: 0.6398 (pmm) cc_final: 0.6195 (pmm)
REVERT: A  452 LYS cc_start: 0.7038 (mmmm) cc_final: 0.6733 (mmtt)
REVERT: B  399 MET cc_start: 0.7144 (ppp) cc_final: 0.6682 (ptp)
REVERT: B  469 GLU cc_start: 0.4491 (OUTLIER) cc_final: 0.3871 (pt0)
  outliers start: 21
  outliers final: 15
  residues processed: 89
  average time/residue: 0.1899
  time to fit residues: 23.9512
Evaluate side-chains
  86 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   40 CYS
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain A residue  164 TRP
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  421 PHE
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain B residue  513 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 94 optimal weight:    4.9990
   chunk 87 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 80 optimal weight:    0.0060
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.7600

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

Flipped N/Q/H residues before XYZ refinement:
A 258 ASN
** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS
** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.3965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8111  Z= 0.197
  Angle     :  0.681  13.068  11049  Z= 0.322
  Chirality :  0.045   0.329   1292
  Planarity :  0.004   0.053   1374
  Dihedral  :  7.028  55.935   1346
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.30 %
    Favored  : 90.70 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 16.97 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.27), residues: 957
  helix:  2.11 (0.47), residues: 131
  sheet: -0.61 (0.27), residues: 333
  loop : -2.09 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 172 
 HIS   0.002   0.001   HIS B 216 
 PHE   0.016   0.001   PHE A 158 
 TYR   0.013   0.001   TYR B 505 
 ARG   0.005   0.001   ARG B 178 

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

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

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1914 Ramachandran restraints generated.
    957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 72
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 ASP cc_start: 0.8699 (p0) cc_final: 0.8291 (p0)
REVERT: A  438 MET cc_start: 0.6420 (pmm) cc_final: 0.6190 (pmm)
REVERT: A  452 LYS cc_start: 0.7099 (mmmm) cc_final: 0.6770 (mmtt)
REVERT: B  469 GLU cc_start: 0.4491 (OUTLIER) cc_final: 0.3912 (pt0)
  outliers start: 20
  outliers final: 14
  residues processed: 86
  average time/residue: 0.1977
  time to fit residues: 24.2546
Evaluate side-chains
  87 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   40 CYS
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain A residue  164 TRP
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  421 PHE
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  301 ILE
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain B residue  513 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 13 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 404 ASN
** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS
** B 284 HIS ** 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 = 0.3977 r_free = 0.3977 target = 0.115291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.093229 restraints weight = 21944.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.093508 restraints weight = 15799.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.093787 restraints weight = 12301.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.4239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8111  Z= 0.239
  Angle     :  0.683  17.884  11049  Z= 0.329
  Chirality :  0.046   0.332   1292
  Planarity :  0.004   0.055   1374
  Dihedral  :  7.063  56.726   1346
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 16.86 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.27), residues: 957
  helix:  2.52 (0.46), residues: 121
  sheet: -0.62 (0.28), residues: 333
  loop : -2.09 (0.26), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 172 
 HIS   0.005   0.001   HIS B 190 
 PHE   0.008   0.001   PHE A 332 
 TYR   0.022   0.001   TYR A 257 
 ARG   0.004   0.001   ARG A 262 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2060.76 seconds
wall clock time: 38 minutes 10.25 seconds (2290.25 seconds total)