Starting phenix.real_space_refine
on Fri Jul 25 21:01:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d6a_27221/07_2025/8d6a_27221.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d6a_27221/07_2025/8d6a_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_27221/07_2025/8d6a_27221.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d6a_27221/07_2025/8d6a_27221.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d6a_27221/07_2025/8d6a_27221.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d6a_27221/07_2025/8d6a_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.94, per 1000 atoms: 0.75
  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: 2.16
  Conformation dependent library (CDL) restraints added in 953.9 milliseconds
  

  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: 1.34
  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: 2.46

  Time building geometry restraints manager: 2.52 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:             6.360
  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:          0.460
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     22.650
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.810
-------------------------------------------------------------------------------
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   8135  Z= 0.143
  Angle     :  0.582   8.908  11112  Z= 0.292
  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 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00653 (   10)
  link_NAG-ASN         : angle       2.87550 (   30)
  link_BETA1-4         : bond        0.00351 (    5)
  link_BETA1-4         : angle       1.23252 (   15)
  hydrogen bonds       : bond        0.25047 (  228)
  hydrogen bonds       : angle       8.70376 (  648)
  SS BOND              : bond        0.00375 (    9)
  SS BOND              : angle       1.28266 (   18)
  covalent geometry    : bond        0.00276 ( 8111)
  covalent geometry    : angle       0.55975 (11049)

*********************** 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  : 0.931 
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: 0.2267
  time to fit residues: 45.9525
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.125896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.102981 restraints weight = 22637.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.102791 restraints weight = 12663.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.103721 restraints weight = 10317.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
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   8135  Z= 0.123
  Angle     :  0.646   9.225  11112  Z= 0.314
  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 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00617 (   10)
  link_NAG-ASN         : angle       2.82420 (   30)
  link_BETA1-4         : bond        0.00297 (    5)
  link_BETA1-4         : angle       1.64465 (   15)
  hydrogen bonds       : bond        0.04857 (  228)
  hydrogen bonds       : angle       6.10311 (  648)
  SS BOND              : bond        0.00371 (    9)
  SS BOND              : angle       0.89925 (   18)
  covalent geometry    : bond        0.00266 ( 8111)
  covalent geometry    : angle       0.62721 (11049)

*********************** 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  : 0.958 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 ASP cc_start: 0.8683 (p0) cc_final: 0.8399 (p0)
  outliers start: 22
  outliers final: 7
  residues processed: 98
  average time/residue: 0.2358
  time to fit residues: 33.3667
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  : 2.134 
-------------------------------------------------------------------------------
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 56 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
D  70 GLN
A 153 HIS
A 167 HIS
A 258 ASN
A 404 ASN
** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS
B 251 GLN
** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.117893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.095918 restraints weight = 22650.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.095488 restraints weight = 18185.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.096016 restraints weight = 13636.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8135  Z= 0.170
  Angle     :  0.681   9.643  11112  Z= 0.334
  Chirality :  0.047   0.390   1292
  Planarity :  0.005   0.057   1374
  Dihedral  :  9.845  75.261   1346
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 14.22 %
    Favored  : 83.37 %
  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: -2.14 (0.25), residues: 957
  helix:  1.95 (0.47), residues: 128
  sheet: -1.31 (0.25), residues: 328
  loop : -2.48 (0.24), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP B 172 
 HIS   0.006   0.001   HIS A 167 
 PHE   0.013   0.001   PHE A 297 
 TYR   0.023   0.002   TYR A 396 
 ARG   0.007   0.001   ARG D 121 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00607 (   10)
  link_NAG-ASN         : angle       2.95697 (   30)
  link_BETA1-4         : bond        0.00368 (    5)
  link_BETA1-4         : angle       1.62126 (   15)
  hydrogen bonds       : bond        0.06285 (  228)
  hydrogen bonds       : angle       5.51990 (  648)
  SS BOND              : bond        0.00830 (    9)
  SS BOND              : angle       1.11905 (   18)
  covalent geometry    : bond        0.00380 ( 8111)
  covalent geometry    : angle       0.66094 (11049)

*********************** 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
  117 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   62 LEU cc_start: 0.9149 (tp) cc_final: 0.8900 (tp)
REVERT: A  177 ASP cc_start: 0.8500 (p0) cc_final: 0.8218 (p0)
REVERT: B  469 GLU cc_start: 0.4716 (OUTLIER) cc_final: 0.4440 (pt0)
  outliers start: 21
  outliers final: 13
  residues processed: 109
  average time/residue: 0.2602
  time to fit residues: 39.7534
Evaluate side-chains
  98 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
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  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  145 SER
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  282 ILE
Chi-restraints excluded: chain B residue  469 GLU
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 75 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 58 optimal weight:    0.3980
   chunk 69 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 35 optimal weight:    6.9990
   chunk 7 optimal weight:    0.0770
   overall best weight:    0.6538

-------------------------------------------------------------------------------
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 191 ASN
** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.117939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.095591 restraints weight = 22167.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.095579 restraints weight = 16509.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.096024 restraints weight = 11960.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.3264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8135  Z= 0.131
  Angle     :  0.638   9.616  11112  Z= 0.314
  Chirality :  0.045   0.347   1292
  Planarity :  0.004   0.058   1374
  Dihedral  :  8.888  70.360   1346
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.78 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 14.91 %
    Favored  : 82.22 %
  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: -1.89 (0.26), residues: 957
  helix:  2.05 (0.47), residues: 131
  sheet: -1.16 (0.26), residues: 335
  loop : -2.32 (0.26), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP B 172 
 HIS   0.007   0.001   HIS A 167 
 PHE   0.011   0.001   PHE A 297 
 TYR   0.014   0.001   TYR A 366 
 ARG   0.002   0.000   ARG A 176 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00653 (   10)
  link_NAG-ASN         : angle       2.94835 (   30)
  link_BETA1-4         : bond        0.00535 (    5)
  link_BETA1-4         : angle       1.69189 (   15)
  hydrogen bonds       : bond        0.05594 (  228)
  hydrogen bonds       : angle       5.30499 (  648)
  SS BOND              : bond        0.00429 (    9)
  SS BOND              : angle       1.08586 (   18)
  covalent geometry    : bond        0.00285 ( 8111)
  covalent geometry    : angle       0.61595 (11049)

*********************** 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
  105 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 80
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   62 LEU cc_start: 0.9108 (tp) cc_final: 0.8863 (tp)
REVERT: A  177 ASP cc_start: 0.8463 (p0) cc_final: 0.8144 (p0)
REVERT: B  453 TRP cc_start: 0.6196 (p90) cc_final: 0.5898 (p90)
REVERT: B  469 GLU cc_start: 0.4746 (OUTLIER) cc_final: 0.4519 (pt0)
REVERT: B  505 TYR cc_start: 0.5228 (m-10) cc_final: 0.4958 (m-10)
  outliers start: 25
  outliers final: 15
  residues processed: 95
  average time/residue: 0.2707
  time to fit residues: 36.3757
Evaluate side-chains
  91 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 1.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  368 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  404 ASN
Chi-restraints excluded: chain A residue  413 VAL
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain B residue  145 SER
Chi-restraints excluded: chain B residue  209 MET
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  282 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   chunk 88 optimal weight:    0.5980
   chunk 58 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 13 optimal weight:   20.0000
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 258 ASN
A 404 ASN
A 478 HIS
** 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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.114084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.092188 restraints weight = 22050.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.091657 restraints weight = 16731.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.092292 restraints weight = 13559.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.3858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8135  Z= 0.178
  Angle     :  0.681   9.886  11112  Z= 0.334
  Chirality :  0.046   0.340   1292
  Planarity :  0.005   0.055   1374
  Dihedral  :  8.394  65.492   1346
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 15.14 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -1.89 (0.26), residues: 957
  helix:  1.85 (0.46), residues: 131
  sheet: -1.07 (0.27), residues: 337
  loop : -2.33 (0.26), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 172 
 HIS   0.003   0.001   HIS A 167 
 PHE   0.012   0.001   PHE A 297 
 TYR   0.014   0.002   TYR A 453 
 ARG   0.004   0.001   ARG D 154 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00619 (   10)
  link_NAG-ASN         : angle       3.03633 (   30)
  link_BETA1-4         : bond        0.00430 (    5)
  link_BETA1-4         : angle       1.77268 (   15)
  hydrogen bonds       : bond        0.06781 (  228)
  hydrogen bonds       : angle       5.36927 (  648)
  SS BOND              : bond        0.00519 (    9)
  SS BOND              : angle       1.25427 (   18)
  covalent geometry    : bond        0.00411 ( 8111)
  covalent geometry    : angle       0.65970 (11049)

*********************** 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
  119 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 83
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 ASP cc_start: 0.8484 (p0) cc_final: 0.8112 (p0)
REVERT: B  464 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6521 (t80)
REVERT: B  469 GLU cc_start: 0.4808 (OUTLIER) cc_final: 0.4524 (pt0)
  outliers start: 36
  outliers final: 21
  residues processed: 104
  average time/residue: 0.1852
  time to fit residues: 27.4803
Evaluate side-chains
  101 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 LEU
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  368 VAL
Chi-restraints excluded: chain A residue  404 ASN
Chi-restraints excluded: chain A residue  413 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  482 LEU
Chi-restraints excluded: chain A residue  499 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  464 PHE
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 13 optimal weight:   20.0000
   chunk 64 optimal weight:    2.9990
   chunk 75 optimal weight:    8.9990
   chunk 61 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0040
   chunk 4 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.6994

-------------------------------------------------------------------------------
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**
B 190 HIS
** B 284 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 = 0.3971 r_free = 0.3971 target = 0.115029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.093170 restraints weight = 21738.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.092881 restraints weight = 15069.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.093314 restraints weight = 12635.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.3978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8135  Z= 0.133
  Angle     :  0.665  15.943  11112  Z= 0.320
  Chirality :  0.046   0.334   1292
  Planarity :  0.005   0.055   1374
  Dihedral  :  8.067  63.157   1346
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.40 %
    Favored  : 90.60 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 17.09 %
    Favored  : 79.93 %
  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: -1.76 (0.27), residues: 957
  helix:  1.94 (0.47), residues: 131
  sheet: -0.98 (0.27), residues: 337
  loop : -2.24 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 470 
 HIS   0.005   0.001   HIS A 478 
 PHE   0.011   0.001   PHE A 332 
 TYR   0.013   0.001   TYR A 334 
 ARG   0.005   0.000   ARG B 178 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00631 (   10)
  link_NAG-ASN         : angle       3.03588 (   30)
  link_BETA1-4         : bond        0.00463 (    5)
  link_BETA1-4         : angle       1.72453 (   15)
  hydrogen bonds       : bond        0.06186 (  228)
  hydrogen bonds       : angle       5.18766 (  648)
  SS BOND              : bond        0.00524 (    9)
  SS BOND              : angle       1.71252 (   18)
  covalent geometry    : bond        0.00294 ( 8111)
  covalent geometry    : angle       0.64088 (11049)

*********************** 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
  100 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 74
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 ASP cc_start: 0.8440 (p0) cc_final: 0.8058 (p0)
REVERT: B  464 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6503 (t80)
  outliers start: 26
  outliers final: 19
  residues processed: 93
  average time/residue: 0.1909
  time to fit residues: 24.8662
Evaluate side-chains
  89 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain A residue  132 LEU
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  368 VAL
Chi-restraints excluded: chain A residue  413 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  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  372 VAL
Chi-restraints excluded: chain B residue  464 PHE
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 73 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0070
   chunk 49 optimal weight:    2.9990
   chunk 93 optimal weight:    0.0070
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    0.4980
   chunk 27 optimal weight:    0.1980
   chunk 58 optimal weight:    9.9990
   chunk 4 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 86 optimal weight:    0.6980
   overall best weight:    0.2616

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

Flipped N/Q/H residues before XYZ refinement:
A 258 ASN
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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.116998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.094612 restraints weight = 22275.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.094956 restraints weight = 16175.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.095608 restraints weight = 12965.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.3956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8135  Z= 0.112
  Angle     :  0.654   9.522  11112  Z= 0.315
  Chirality :  0.045   0.332   1292
  Planarity :  0.004   0.055   1374
  Dihedral  :  7.506  59.845   1346
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 17.20 %
    Favored  : 79.82 %
  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: -1.61 (0.27), residues: 957
  helix:  2.11 (0.47), residues: 131
  sheet: -0.78 (0.28), residues: 329
  loop : -2.23 (0.26), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 172 
 HIS   0.005   0.001   HIS B 216 
 PHE   0.009   0.001   PHE B 459 
 TYR   0.009   0.001   TYR B 379 
 ARG   0.009   0.001   ARG A 176 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00648 (   10)
  link_NAG-ASN         : angle       3.02523 (   30)
  link_BETA1-4         : bond        0.00433 (    5)
  link_BETA1-4         : angle       1.71765 (   15)
  hydrogen bonds       : bond        0.05069 (  228)
  hydrogen bonds       : angle       4.89914 (  648)
  SS BOND              : bond        0.00448 (    9)
  SS BOND              : angle       1.34548 (   18)
  covalent geometry    : bond        0.00234 ( 8111)
  covalent geometry    : angle       0.63102 (11049)

*********************** 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
  103 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 77
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 ASP cc_start: 0.8529 (p0) cc_final: 0.8188 (p0)
REVERT: B  399 MET cc_start: 0.7074 (ptm) cc_final: 0.6861 (ptm)
REVERT: B  464 PHE cc_start: 0.7279 (OUTLIER) cc_final: 0.6528 (t80)
  outliers start: 26
  outliers final: 18
  residues processed: 93
  average time/residue: 0.1946
  time to fit residues: 25.4554
Evaluate side-chains
  88 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  164 TRP
Chi-restraints excluded: chain A residue  258 ASN
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  404 ASN
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  499 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  464 PHE
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 32 optimal weight:    0.2980
   chunk 52 optimal weight:    0.8980
   chunk 73 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 38 optimal weight:    7.9990
   chunk 63 optimal weight:    4.9990
   chunk 41 optimal weight:    8.9990
   chunk 26 optimal weight:    6.9990
   chunk 59 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 83 optimal weight:    0.0980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.115533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.093321 restraints weight = 22054.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.093921 restraints weight = 15650.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.094827 restraints weight = 10731.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.4223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8135  Z= 0.136
  Angle     :  0.656   9.438  11112  Z= 0.318
  Chirality :  0.045   0.333   1292
  Planarity :  0.005   0.065   1374
  Dihedral  :  7.358  57.111   1346
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.61 %
    Favored  : 90.39 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 17.89 %
    Favored  : 79.47 %
  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: -1.64 (0.27), residues: 957
  helix:  2.05 (0.47), residues: 131
  sheet: -0.77 (0.28), residues: 329
  loop : -2.26 (0.26), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 470 
 HIS   0.003   0.001   HIS B 216 
 PHE   0.010   0.001   PHE A 297 
 TYR   0.022   0.001   TYR A 366 
 ARG   0.010   0.001   ARG A 176 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00623 (   10)
  link_NAG-ASN         : angle       3.13571 (   30)
  link_BETA1-4         : bond        0.00447 (    5)
  link_BETA1-4         : angle       1.78353 (   15)
  hydrogen bonds       : bond        0.05527 (  228)
  hydrogen bonds       : angle       4.97158 (  648)
  SS BOND              : bond        0.00496 (    9)
  SS BOND              : angle       1.36159 (   18)
  covalent geometry    : bond        0.00304 ( 8111)
  covalent geometry    : angle       0.63190 (11049)

*********************** 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
  93 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 ASP cc_start: 0.8602 (p0) cc_final: 0.8247 (p0)
REVERT: B  464 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.6538 (t80)
  outliers start: 23
  outliers final: 18
  residues processed: 89
  average time/residue: 0.2029
  time to fit residues: 25.3529
Evaluate side-chains
  86 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  189 VAL
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  404 ASN
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  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  372 VAL
Chi-restraints excluded: chain B residue  464 PHE
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 83 optimal weight:    0.7980
   chunk 89 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0060
   chunk 34 optimal weight:    0.8980
   chunk 7 optimal weight:    0.2980
   chunk 50 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
A 258 ASN
B 190 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.116018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.093633 restraints weight = 22421.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.093880 restraints weight = 15206.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.094588 restraints weight = 12624.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.4302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8135  Z= 0.121
  Angle     :  0.656   9.480  11112  Z= 0.315
  Chirality :  0.045   0.332   1292
  Planarity :  0.004   0.053   1374
  Dihedral  :  6.977  54.113   1346
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.30 %
    Favored  : 90.70 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 17.66 %
    Favored  : 79.82 %
  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:  2.10 (0.47), residues: 131
  sheet: -0.71 (0.28), residues: 329
  loop : -2.21 (0.26), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 470 
 HIS   0.003   0.001   HIS B 216 
 PHE   0.010   0.001   PHE A 297 
 TYR   0.018   0.001   TYR B 505 
 ARG   0.012   0.001   ARG A 176 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00621 (   10)
  link_NAG-ASN         : angle       3.24864 (   30)
  link_BETA1-4         : bond        0.00470 (    5)
  link_BETA1-4         : angle       1.80334 (   15)
  hydrogen bonds       : bond        0.05220 (  228)
  hydrogen bonds       : angle       4.86900 (  648)
  SS BOND              : bond        0.00435 (    9)
  SS BOND              : angle       1.35999 (   18)
  covalent geometry    : bond        0.00263 ( 8111)
  covalent geometry    : angle       0.62951 (11049)

*********************** 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
  95 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 73
  time to evaluate  : 0.826 
Fit side-chains
   revert: symmetry clash
REVERT: A  177 ASP cc_start: 0.8733 (p0) cc_final: 0.8394 (p0)
REVERT: A  452 LYS cc_start: 0.7318 (mmmm) cc_final: 0.6682 (mmtt)
  outliers start: 22
  outliers final: 19
  residues processed: 87
  average time/residue: 0.2154
  time to fit residues: 26.2187
Evaluate side-chains
  86 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  164 TRP
Chi-restraints excluded: chain A residue  189 VAL
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  413 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  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  372 VAL
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 77 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 78 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   chunk 87 optimal weight:    0.1980
   chunk 81 optimal weight:    0.0770
   chunk 56 optimal weight:    0.0970
   chunk 55 optimal weight:    0.0870
   chunk 63 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.2514

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

Flipped N/Q/H residues before XYZ refinement:
A 258 ASN
A 404 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.116677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.094473 restraints weight = 22032.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.095105 restraints weight = 14749.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.095675 restraints weight = 10471.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.4339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   8135  Z= 0.115
  Angle     :  0.656   9.424  11112  Z= 0.316
  Chirality :  0.045   0.332   1292
  Planarity :  0.005   0.058   1374
  Dihedral  :  6.778  53.457   1346
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.30 %
    Favored  : 90.70 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 18.12 %
    Favored  : 79.70 %
  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: -1.51 (0.27), residues: 957
  helix:  2.14 (0.47), residues: 131
  sheet: -0.67 (0.28), residues: 331
  loop : -2.19 (0.26), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 172 
 HIS   0.003   0.000   HIS B 216 
 PHE   0.008   0.001   PHE B 459 
 TYR   0.011   0.001   TYR A 334 
 ARG   0.014   0.001   ARG A 395 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00636 (   10)
  link_NAG-ASN         : angle       3.22595 (   30)
  link_BETA1-4         : bond        0.00473 (    5)
  link_BETA1-4         : angle       1.81001 (   15)
  hydrogen bonds       : bond        0.04892 (  228)
  hydrogen bonds       : angle       4.84207 (  648)
  SS BOND              : bond        0.00439 (    9)
  SS BOND              : angle       1.24115 (   18)
  covalent geometry    : bond        0.00245 ( 8111)
  covalent geometry    : angle       0.63090 (11049)

********************** 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: 19
    poor density    : 73
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 19
  outliers final: 17
  residues processed: 84
  average time/residue: 0.1977
  time to fit residues: 23.3014
Evaluate side-chains
  85 residues out of total 872 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  258 ASN
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  413 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  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  372 VAL
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 57 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0370
   chunk 83 optimal weight:    0.2980
   chunk 59 optimal weight:    0.0670
   chunk 80 optimal weight:    6.9990
   chunk 42 optimal weight:    0.2980
   chunk 75 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 31 optimal weight:    0.1980
   chunk 63 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.1796

-------------------------------------------------------------------------------
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 226 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.117454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.095473 restraints weight = 22267.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.095925 restraints weight = 15014.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.096462 restraints weight = 10733.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.4333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   8135  Z= 0.111
  Angle     :  0.652   9.380  11112  Z= 0.314
  Chirality :  0.045   0.333   1292
  Planarity :  0.004   0.054   1374
  Dihedral  :  6.596  53.109   1346
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 18.23 %
    Favored  : 79.70 %
  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: -1.42 (0.27), residues: 957
  helix:  2.10 (0.47), residues: 134
  sheet: -0.53 (0.29), residues: 319
  loop : -2.15 (0.26), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 470 
 HIS   0.003   0.000   HIS B 216 
 PHE   0.009   0.001   PHE A 297 
 TYR   0.013   0.001   TYR A 257 
 ARG   0.009   0.001   ARG A 395 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00638 (   10)
  link_NAG-ASN         : angle       3.22462 (   30)
  link_BETA1-4         : bond        0.00463 (    5)
  link_BETA1-4         : angle       1.80371 (   15)
  hydrogen bonds       : bond        0.04622 (  228)
  hydrogen bonds       : angle       4.74479 (  648)
  SS BOND              : bond        0.00410 (    9)
  SS BOND              : angle       1.17382 (   18)
  covalent geometry    : bond        0.00235 ( 8111)
  covalent geometry    : angle       0.62648 (11049)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3405.29 seconds
wall clock time: 62 minutes 30.00 seconds (3750.00 seconds total)