Starting phenix.real_space_refine
on Sun May 11 18:12:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vlv_43345/05_2025/8vlv_43345.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vlv_43345/05_2025/8vlv_43345.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vlv_43345/05_2025/8vlv_43345.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vlv_43345/05_2025/8vlv_43345.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vlv_43345/05_2025/8vlv_43345.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vlv_43345/05_2025/8vlv_43345.cif"
  }
  resolution = 3.49
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.042
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      35      5.16       5
     C    5452      2.51       5
     N    1340      2.21       5
     O    1438      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8265
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4104
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 542, 4079
          Classifications: {'peptide': 542}
          Incomplete info: {'truncation_to_alanine': 63}
          Link IDs: {'PTRANS': 25, 'TRANS': 516}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 242
          Unresolved non-hydrogen angles: 305
          Unresolved non-hydrogen dihedrals: 208
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 8, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 130
      Conformer: "B"
        Number of residues, atoms: 542, 4079
          Classifications: {'peptide': 542}
          Incomplete info: {'truncation_to_alanine': 63}
          Link IDs: {'PTRANS': 25, 'TRANS': 516}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 242
          Unresolved non-hydrogen angles: 305
          Unresolved non-hydrogen dihedrals: 208
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 8, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 130
          bond proxies already assigned to first conformer: 4163
    Chain: "B"
      Number of atoms: 4035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 543, 4035
          Classifications: {'peptide': 543}
          Incomplete info: {'truncation_to_alanine': 82}
          Link IDs: {'PTRANS': 24, 'TRANS': 518}
          Chain breaks: 4
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 295
          Unresolved non-hydrogen angles: 368
          Unresolved non-hydrogen dihedrals: 246
          Unresolved non-hydrogen chiralities: 24
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 13, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 152
    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: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  ATRP A 344 " occ=0.52
      ... (26 atoms not shown)
      pdb=" CH2BTRP A 344 " occ=0.48
    residue:
      pdb=" N  AARG A 412 " occ=0.42
      ... (20 atoms not shown)
      pdb=" NH2BARG A 412 " occ=0.58
  Time building chain proxies: 8.38, per 1000 atoms: 1.01
  Number of scatterers: 8265
  At special positions: 0
  Unit cell: (108.42, 95.91, 104.25, 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      35     16.00
     O    1438      8.00
     N    1340      7.00
     C    5452      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 104 " - pdb=" SG  CYS A 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 151 " - pdb=" SG  CYS A 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 443 " - pdb=" SG  CYS A 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 104 " - pdb=" SG  CYS B 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 151 " - pdb=" SG  CYS B 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 443 " - pdb=" SG  CYS B 462 " 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-ASN
      " NAG A 701 " - " ASN A  94 "
      " NAG A 702 " - " ASN A 162 "
      " NAG A 703 " - " ASN A 461 "
      " NAG B 701 " - " ASN B  94 "
      " NAG B 702 " - " ASN B 142 "
      " NAG B 703 " - " ASN B 162 "
      " NAG B 704 " - " ASN B 461 "
      " NAG C   1 " - " ASN A 142 "
  Time building additional restraints: 2.40
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2012

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 4 sheets defined
      54.1% alpha, 7.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 194 through 202
      removed outlier: 3.964A  pdb=" N   ILE A 200 " --> pdb=" O   ILE A 196 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   LEU A 202 " --> pdb=" O   PHE A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 223
      removed outlier: 3.694A  pdb=" N   ASP A 219 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 287
    Processing helix  chain 'A' and resid 288 through 292
      removed outlier: 3.707A  pdb=" N   TYR A 292 " --> pdb=" O   GLY A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 308
    Processing helix  chain 'A' and resid 309 through 332
      removed outlier: 3.527A  pdb=" N   PHE A 313 " --> pdb=" O   VAL A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 357
    Processing helix  chain 'A' and resid 375 through 394
      removed outlier: 3.566A  pdb=" N   PHE A 394 " --> pdb=" O   LEU A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 416
      removed outlier: 3.650A  pdb=" N   THR A 415 " --> pdb=" O   LEU A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 438
    Processing helix  chain 'A' and resid 454 through 458
      removed outlier: 3.523A  pdb=" N   LYS A 458 " --> pdb=" O   ASP A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 476
      removed outlier: 3.544A  pdb=" N   ILE A 470 " --> pdb=" O   ALA A 466 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   ASP A 471 " --> pdb=" O   ALA A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 489
      removed outlier: 4.036A  pdb=" N   VAL A 488 " --> pdb=" O   SER A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 524
      removed outlier: 3.607A  pdb=" N   ILE A 505 " --> pdb=" O   ILE A 501 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   TYR A 524 " --> pdb=" O   ILE A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 551
      removed outlier: 4.323A  pdb=" N   ILE A 531 " --> pdb=" O   ARG A 527 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   LEU A 532 " --> pdb=" O   THR A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 590
      Proline residue:  A 587  - end of helix
    Processing helix  chain 'A' and resid 602 through 605
      removed outlier: 3.655A  pdb=" N   MET A 605 " --> pdb=" O   TYR A 602 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 602 through 605'
    Processing helix  chain 'A' and resid 606 through 617
    Processing helix  chain 'A' and resid 632 through 657
    Processing helix  chain 'B' and resid 195 through 228
    Processing helix  chain 'B' and resid 269 through 287
    Processing helix  chain 'B' and resid 288 through 292
      removed outlier: 3.778A  pdb=" N   TYR B 292 " --> pdb=" O   GLY B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 307
    Processing helix  chain 'B' and resid 308 through 331
      removed outlier: 3.810A  pdb=" N   TRP B 312 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 357
    Processing helix  chain 'B' and resid 375 through 394
    Processing helix  chain 'B' and resid 414 through 416
      No H-bonds generated for 'chain 'B' and resid 414 through 416'
    Processing helix  chain 'B' and resid 417 through 438
      removed outlier: 3.526A  pdb=" N   TRP B 421 " --> pdb=" O   SER B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 458
      removed outlier: 3.734A  pdb=" N   PHE B 456 " --> pdb=" O   ILE B 453 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 475
      removed outlier: 3.524A  pdb=" N   ASP B 471 " --> pdb=" O   ALA B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 486 through 491
    Processing helix  chain 'B' and resid 503 through 524
      removed outlier: 3.750A  pdb=" N   TYR B 524 " --> pdb=" O   ILE B 520 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 527 through 551
    Processing helix  chain 'B' and resid 567 through 590
      Proline residue:  B 587  - end of helix
    Processing helix  chain 'B' and resid 600 through 606
      removed outlier: 3.607A  pdb=" N   ASN B 606 " --> pdb=" O   TYR B 602 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 606 through 617
    Processing helix  chain 'B' and resid 632 through 657
      removed outlier: 3.584A  pdb=" N   HIS B 636 " --> pdb=" O   SER B 632 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   VAL B 642 " --> pdb=" O   THR B 638 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 132
      removed outlier: 3.695A  pdb=" N   SER A 125 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   LEU A 165 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 5.676A  pdb=" N   LEU A  85 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   VAL A 167 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   HIS A  87 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU A 166 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 115
      removed outlier: 3.725A  pdb=" N   GLN A 110 " --> pdb=" O   TRP A  99 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   VAL A  97 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   ASN A 114 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   LEU A  95 " --> pdb=" O   ASN A 114 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   CYS A 151 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   ASP A 143 " --> pdb=" O   GLU A 149 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   GLU A 149 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 127 through 132
      removed outlier: 7.555A  pdb=" N   LEU B 165 " --> pdb=" O   LEU B  83 " (cutoff:3.500A)
      removed outlier: 5.881A  pdb=" N   LEU B  85 " --> pdb=" O   LEU B 165 " (cutoff:3.500A)
      removed outlier: 7.352A  pdb=" N   VAL B 167 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   HIS B  87 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
      removed outlier: 8.678A  pdb=" N   ASN B 169 " --> pdb=" O   HIS B  87 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 110 through 115
      removed outlier: 3.881A  pdb=" N   LEU B 112 " --> pdb=" O   VAL B  97 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   VAL B  97 " --> pdb=" O   LEU B 112 " (cutoff:3.500A)
      removed outlier: 5.808A  pdb=" N   ASN B 114 " --> pdb=" O   LEU B  95 " (cutoff:3.500A)
      removed outlier: 7.773A  pdb=" N   LEU B  95 " --> pdb=" O   ASN B 114 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   THR B  96 " --> pdb=" O   ASN B 142 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   CYS B 151 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)

    463 hydrogen bonds defined for protein.
    1342 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: 2.44

  Time building geometry restraints manager: 2.76 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2522
        1.34 -     1.46: 2110
        1.46 -     1.58: 3814
        1.58 -     1.70: 0
        1.70 -     1.81: 46
  Bond restraints: 8492
  Sorted by residual:
  bond pdb=" C1  NAG B 702 "
       pdb=" O5  NAG B 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.476 -0.070 2.00e-02 2.50e+03 1.21e+01
  bond pdb=" C1  NAG A 703 "
       pdb=" O5  NAG A 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.13e+00
  bond pdb=" C1  NAG B 703 "
       pdb=" O5  NAG B 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.98e+00
  bond pdb=" C1  NAG A 702 "
       pdb=" O5  NAG A 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.78e+00
  bond pdb=" C1  NAG A 701 "
       pdb=" O5  NAG A 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.76e+00
  ... (remaining 8487 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.28: 11187
        1.28 -     2.56: 345
        2.56 -     3.84: 74
        3.84 -     5.12: 18
        5.12 -     6.40: 8
  Bond angle restraints: 11632
  Sorted by residual:
  angle pdb=" C   GLY B 613 "
        pdb=" N   HIS B 614 "
        pdb=" CA  HIS B 614 "
      ideal   model   delta    sigma   weight residual
     121.14  116.35    4.79 1.75e+00 3.27e-01 7.51e+00
  angle pdb=" N   TRP A 418 "
        pdb=" CA  TRP A 418 "
        pdb=" C   TRP A 418 "
      ideal   model   delta    sigma   weight residual
     109.81  115.81   -6.00 2.21e+00 2.05e-01 7.38e+00
  angle pdb=" C   GLY A 613 "
        pdb=" N   HIS A 614 "
        pdb=" CA  HIS A 614 "
      ideal   model   delta    sigma   weight residual
     121.14  116.55    4.59 1.75e+00 3.27e-01 6.87e+00
  angle pdb=" C   PHE A 600 "
        pdb=" N   PHE A 601 "
        pdb=" CA  PHE A 601 "
      ideal   model   delta    sigma   weight residual
     122.06  117.79    4.27 1.86e+00 2.89e-01 5.27e+00
  angle pdb=" C   GLY A 452 "
        pdb=" N   ILE A 453 "
        pdb=" CA  ILE A 453 "
      ideal   model   delta    sigma   weight residual
     121.97  125.90   -3.93 1.80e+00 3.09e-01 4.76e+00
  ... (remaining 11627 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.75: 4639
       22.75 -    45.49: 276
       45.49 -    68.24: 33
       68.24 -    90.99: 17
       90.99 -   113.73: 6
  Dihedral angle restraints: 4971
    sinusoidal: 1831
      harmonic: 3140
  Sorted by residual:
  dihedral pdb=" CB  CYS B 443 "
           pdb=" SG  CYS B 443 "
           pdb=" SG  CYS B 462 "
           pdb=" CB  CYS B 462 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  151.90  -58.90     1      1.00e+01 1.00e-02 4.64e+01
  dihedral pdb=" CA  ASN B  94 "
           pdb=" C   ASN B  94 "
           pdb=" N   LEU B  95 "
           pdb=" CA  LEU B  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.73  -20.27     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" C3  NAG B 702 "
           pdb=" C1  NAG B 702 "
           pdb=" C2  NAG B 702 "
           pdb=" O5  NAG B 702 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -55.55   58.18 -113.73     1      3.00e+01 1.11e-03 1.50e+01
  ... (remaining 4968 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1267
       0.069 -    0.138: 117
       0.138 -    0.208: 4
       0.208 -    0.277: 0
       0.277 -    0.346: 1
  Chirality restraints: 1389
  Sorted by residual:
  chirality pdb=" C1  NAG B 701 "
            pdb=" ND2 ASN B  94 "
            pdb=" C2  NAG B 701 "
            pdb=" O5  NAG B 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.05   -0.35 2.00e-01 2.50e+01 2.99e+00
  chirality pdb=" C2  NAG C   2 "
            pdb=" C1  NAG C   2 "
            pdb=" C3  NAG C   2 "
            pdb=" N2  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.31   -0.18 2.00e-01 2.50e+01 8.06e-01
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 142 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.23   -0.17 2.00e-01 2.50e+01 7.27e-01
  ... (remaining 1386 not shown)

  Planarity restraints: 1434
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  92 "    0.010 2.00e-02 2.50e+03   1.35e-02 4.54e+00
        pdb=" CG  TRP B  92 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  92 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  92 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  92 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  92 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  92 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  92 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  92 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  92 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 606 "   -0.007 2.00e-02 2.50e+03   1.44e-02 2.08e+00
        pdb=" C   ASN A 606 "    0.025 2.00e-02 2.50e+03
        pdb=" O   ASN A 606 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   SER A 607 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 322 "   -0.014 2.00e-02 2.50e+03   1.09e-02 2.08e+00
        pdb=" CG  PHE B 322 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 322 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 322 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 322 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 322 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 322 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1431 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 476
        2.73 -     3.27: 8561
        3.27 -     3.82: 13773
        3.82 -     4.36: 14986
        4.36 -     4.90: 27138
  Nonbonded interactions: 64934
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B 391 "
            pdb=" NE2 GLN B 420 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" NH1 ARG A 275 "
            pdb=" O   GLY A 604 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" O   TYR B 105 "
            pdb=" ND1 HIS B 106 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" ND2 ASN A 506 "
            pdb=" O   TRP A 566 "
     model   vdw
     2.281 3.120
  nonbonded pdb=" O   ARG A 269 "
            pdb=" OG1 THR A 273 "
     model   vdw
     2.285 3.040
  ... (remaining 64929 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 'A' and ((resid 76 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 77 through 90 or (resid 91 through 92 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 93 through 118 or (resid 119 through 121 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 122 through 146 o \ 
r (resid 147 through 150 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 151 through 169 or (resid 170 and (name N or name CA or name C or nam \ 
e O or name CB )) or (resid 175 through 176 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 177 through 179 or (resid 180 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 181 through 192 or (resid 194 thro \ 
ugh 200 and (name N or name CA or name C or name O or name CB )) or resid 201 or \ 
 (resid 202 through 223 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 266 or (resid 267 and (name N or name CA or name C or name O or name C \ 
B )) or resid 268 through 329 or (resid 330 through 331 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 332 through 343 or resid 345 through 4 \ 
11 or resid 413 through 492 or (resid 493 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 494 through 552 or (resid 553 through 554 and (name  \ 
N or name CA or name C or name O or name CB )) or resid 555 or (resid 556 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 557 through 589 or ( \ 
resid 590 and (name N or name CA or name C or name O or name CB )) or resid 591  \ 
or (resid 592 and (name N or name CA or name C or name O or name CB )) or resid  \ 
593 through 597 or (resid 598 and (name N or name CA or name C or name O or name \ 
 CB )) or resid 599 through 604 or (resid 605 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 606 through 625 or (resid 626 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 627 through 628 or (resid 629 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 630 through 633  \ 
or (resid 634 through 635 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 636 through 654 or (resid 655 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 656 through 661 or resid 701 through 703))
  selection = (chain 'B' and (resid 76 through 91 or (resid 92 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 93 through 101 or (resid 102 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 103 through 116 or (resid 117  \ 
and (name N or name CA or name C or name O or name CB )) or resid 118 through 14 \ 
3 or (resid 144 through 150 and (name N or name CA or name C or name O or name C \ 
B )) or resid 151 through 167 or (resid 168 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 169 through 184 or (resid 185 through 186 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 187 through 192 or (re \ 
sid 194 through 200 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 201 through 223 or resid 266 through 336 or (resid 337 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 338 through 343 or resid 345 thro \ 
ugh 362 or (resid 363 and (name N or name CA or name C or name O or name CB )) o \ 
r resid 364 through 395 or (resid 396 and (name N or name CA or name C or name O \ 
 or name CB )) or resid 397 through 400 or (resid 401 through 402 and (name N or \ 
 name CA or name C or name O or name CB )) or (resid 408 through 410 and (name N \ 
 or name CA or name C or name O or name CB )) or resid 411 or resid 413 through  \ 
454 or (resid 455 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 456 through 661 or resid 702 through 704))
}

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=0.42 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     25.600
  Find NCS groups from input model:        0.400
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
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   0.070   8507  Z= 0.150
  Angle     :  0.575   9.412  11671  Z= 0.290
  Chirality :  0.042   0.346   1389
  Planarity :  0.004   0.036   1426
  Dihedral  : 15.449 113.732   2941
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.25 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.27), residues: 1075
  helix:  2.48 (0.22), residues: 521
  sheet: -0.63 (0.56), residues: 113
  loop : -1.76 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.001   TRP B  92 
 HIS   0.003   0.001   HIS B 614 
 PHE   0.024   0.001   PHE B 322 
 TYR   0.016   0.001   TYR B 570 
 ARG   0.005   0.000   ARG A 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00601 (    8)
  link_NAG-ASN         : angle       2.26535 (   24)
  link_BETA1-4         : bond        0.00022 (    1)
  link_BETA1-4         : angle       1.51834 (    3)
  hydrogen bonds       : bond        0.13223 (  463)
  hydrogen bonds       : angle       5.91122 ( 1342)
  SS BOND              : bond        0.00125 (    6)
  SS BOND              : angle       1.29305 (   12)
  covalent geometry    : bond        0.00326 ( 8492)
  covalent geometry    : angle       0.56423 (11632)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.938 
Fit side-chains
REVERT: A  159 GLU cc_start: 0.8479 (tt0) cc_final: 0.8133 (tt0)
REVERT: B  341 LYS cc_start: 0.7443 (tttt) cc_final: 0.7240 (mtpt)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1698
  time to fit residues: 21.9536
Evaluate side-chains
  70 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0770
   chunk 55 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 98 optimal weight:    0.8980
   overall best weight:    0.7738

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

Flipped N/Q/H residues before XYZ refinement:
** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 483 HIS
** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 630 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.138246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.115029 restraints weight = 31243.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 3.51
r_work: 0.3189 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3181
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3181
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.0775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8507  Z= 0.156
  Angle     :  0.596   9.505  11671  Z= 0.297
  Chirality :  0.043   0.320   1389
  Planarity :  0.004   0.060   1426
  Dihedral  :  9.415  96.675   1344
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  5.99 %
    Favored  : 93.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.27), residues: 1075
  helix:  2.36 (0.22), residues: 524
  sheet: -0.59 (0.54), residues: 113
  loop : -1.70 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP B  92 
 HIS   0.005   0.001   HIS B 483 
 PHE   0.024   0.001   PHE B 322 
 TYR   0.018   0.001   TYR B 570 
 ARG   0.005   0.000   ARG A 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00577 (    8)
  link_NAG-ASN         : angle       2.71326 (   24)
  link_BETA1-4         : bond        0.00811 (    1)
  link_BETA1-4         : angle       1.86930 (    3)
  hydrogen bonds       : bond        0.03832 (  463)
  hydrogen bonds       : angle       4.59910 ( 1342)
  SS BOND              : bond        0.00146 (    6)
  SS BOND              : angle       1.05338 (   12)
  covalent geometry    : bond        0.00368 ( 8492)
  covalent geometry    : angle       0.58270 (11632)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.839 
Fit side-chains
REVERT: B  325 MET cc_start: 0.8333 (ttm) cc_final: 0.8061 (ttt)
  outliers start: 4
  outliers final: 3
  residues processed: 75
  average time/residue: 0.1855
  time to fit residues: 20.8546
Evaluate side-chains
  69 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  627 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 107 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 88 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 28 optimal weight:    0.4980
   chunk 16 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 93 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.138019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.114816 restraints weight = 32770.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 3.77
r_work: 0.3182 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3181
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3181
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.0971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8507  Z= 0.135
  Angle     :  0.562  10.168  11671  Z= 0.280
  Chirality :  0.043   0.401   1389
  Planarity :  0.004   0.039   1426
  Dihedral  :  7.917  93.819   1344
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  9.24 %
    Favored  : 89.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.27), residues: 1075
  helix:  2.40 (0.22), residues: 524
  sheet: -0.38 (0.55), residues: 111
  loop : -1.70 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B  92 
 HIS   0.002   0.001   HIS B 135 
 PHE   0.021   0.001   PHE A 322 
 TYR   0.017   0.001   TYR B 570 
 ARG   0.004   0.000   ARG A 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00581 (    8)
  link_NAG-ASN         : angle       2.80177 (   24)
  link_BETA1-4         : bond        0.00335 (    1)
  link_BETA1-4         : angle       1.93947 (    3)
  hydrogen bonds       : bond        0.03399 (  463)
  hydrogen bonds       : angle       4.28399 ( 1342)
  SS BOND              : bond        0.00116 (    6)
  SS BOND              : angle       0.95374 (   12)
  covalent geometry    : bond        0.00317 ( 8492)
  covalent geometry    : angle       0.54661 (11632)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.836 
Fit side-chains
REVERT: A  159 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8258 (tt0)
REVERT: B  325 MET cc_start: 0.8370 (ttm) cc_final: 0.8095 (ttt)
REVERT: B  510 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8089 (ttp)
  outliers start: 8
  outliers final: 5
  residues processed: 79
  average time/residue: 0.1557
  time to fit residues: 18.7512
Evaluate side-chains
  77 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain B residue  510 MET
Chi-restraints excluded: chain B residue  545 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 66 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 42 optimal weight:    0.3980
   chunk 0 optimal weight:    6.9990
   chunk 86 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 85 optimal weight:    0.0970
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.136708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.112678 restraints weight = 38960.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 4.72
r_work: 0.3116 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3120
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3120
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.1104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8507  Z= 0.153
  Angle     :  0.572   9.670  11671  Z= 0.285
  Chirality :  0.042   0.345   1389
  Planarity :  0.004   0.039   1426
  Dihedral  :  7.748  92.431   1344
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 10.74 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.27), residues: 1075
  helix:  2.35 (0.22), residues: 526
  sheet: -0.30 (0.55), residues: 113
  loop : -1.66 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 647 
 HIS   0.003   0.001   HIS B 135 
 PHE   0.022   0.001   PHE B 322 
 TYR   0.018   0.001   TYR B 570 
 ARG   0.004   0.000   ARG A 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00566 (    8)
  link_NAG-ASN         : angle       2.70419 (   24)
  link_BETA1-4         : bond        0.00247 (    1)
  link_BETA1-4         : angle       1.95250 (    3)
  hydrogen bonds       : bond        0.03425 (  463)
  hydrogen bonds       : angle       4.23219 ( 1342)
  SS BOND              : bond        0.00149 (    6)
  SS BOND              : angle       0.84939 (   12)
  covalent geometry    : bond        0.00362 ( 8492)
  covalent geometry    : angle       0.55816 (11632)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.881 
Fit side-chains
REVERT: A  159 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8171 (tt0)
REVERT: A  379 ARG cc_start: 0.8653 (tpp80) cc_final: 0.8431 (tpp80)
REVERT: A  652 TYR cc_start: 0.8599 (t80) cc_final: 0.8265 (t80)
REVERT: B  325 MET cc_start: 0.8468 (ttm) cc_final: 0.8182 (ttt)
REVERT: B  510 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8215 (ttp)
  outliers start: 10
  outliers final: 8
  residues processed: 73
  average time/residue: 0.1756
  time to fit residues: 19.0410
Evaluate side-chains
  77 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  541 ILE
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain B residue  510 MET
Chi-restraints excluded: chain B residue  545 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 105 optimal weight:    6.9990
   chunk 81 optimal weight:    0.8980
   chunk 104 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9990
   chunk 106 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 24 optimal weight:    0.4980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.136395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.112786 restraints weight = 32808.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 4.00
r_work: 0.3139 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3143
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3143 r_free = 0.3143    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3143 r_free = 0.3143    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3143
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8507  Z= 0.154
  Angle     :  0.568   9.493  11671  Z= 0.283
  Chirality :  0.042   0.326   1389
  Planarity :  0.004   0.038   1426
  Dihedral  :  7.579  91.119   1344
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 11.74 %
    Favored  : 86.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.27), residues: 1075
  helix:  2.38 (0.22), residues: 526
  sheet: -0.21 (0.56), residues: 113
  loop : -1.65 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 647 
 HIS   0.003   0.001   HIS B 135 
 PHE   0.022   0.001   PHE B 322 
 TYR   0.019   0.001   TYR B 570 
 ARG   0.004   0.000   ARG A 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00587 (    8)
  link_NAG-ASN         : angle       2.69257 (   24)
  link_BETA1-4         : bond        0.00315 (    1)
  link_BETA1-4         : angle       1.96491 (    3)
  hydrogen bonds       : bond        0.03409 (  463)
  hydrogen bonds       : angle       4.17983 ( 1342)
  SS BOND              : bond        0.00269 (    6)
  SS BOND              : angle       0.77666 (   12)
  covalent geometry    : bond        0.00365 ( 8492)
  covalent geometry    : angle       0.55398 (11632)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.819 
Fit side-chains
REVERT: A  159 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8154 (tt0)
REVERT: A  652 TYR cc_start: 0.8619 (t80) cc_final: 0.8212 (t80)
REVERT: B  510 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8160 (ttp)
  outliers start: 12
  outliers final: 8
  residues processed: 79
  average time/residue: 0.1713
  time to fit residues: 20.1393
Evaluate side-chains
  78 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  541 ILE
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain B residue  510 MET
Chi-restraints excluded: chain B residue  545 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 58 optimal weight:    0.1980
   chunk 77 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 420 GLN
** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 624 GLN ** 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 = 0.3663 r_free = 0.3663 target = 0.134403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.110727 restraints weight = 25740.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 2.74
r_work: 0.3158 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3154
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3154
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   8507  Z= 0.214
  Angle     :  0.619   9.432  11671  Z= 0.311
  Chirality :  0.044   0.309   1389
  Planarity :  0.004   0.039   1426
  Dihedral  :  7.663  90.953   1344
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 12.36 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.26), residues: 1075
  helix:  2.19 (0.22), residues: 526
  sheet: -0.47 (0.54), residues: 114
  loop : -1.77 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 647 
 HIS   0.004   0.001   HIS B 135 
 PHE   0.025   0.002   PHE B 322 
 TYR   0.021   0.002   TYR B 570 
 ARG   0.007   0.000   ARG A 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00595 (    8)
  link_NAG-ASN         : angle       2.71432 (   24)
  link_BETA1-4         : bond        0.00282 (    1)
  link_BETA1-4         : angle       2.13508 (    3)
  hydrogen bonds       : bond        0.03814 (  463)
  hydrogen bonds       : angle       4.29878 ( 1342)
  SS BOND              : bond        0.00226 (    6)
  SS BOND              : angle       0.82427 (   12)
  covalent geometry    : bond        0.00512 ( 8492)
  covalent geometry    : angle       0.60633 (11632)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.819 
Fit side-chains
REVERT: A  159 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8097 (tt0)
REVERT: B  510 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8109 (ttp)
  outliers start: 15
  outliers final: 12
  residues processed: 76
  average time/residue: 0.1545
  time to fit residues: 17.8985
Evaluate side-chains
  77 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  541 ILE
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  510 MET
Chi-restraints excluded: chain B residue  545 ILE
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 99 optimal weight:    0.5980
   chunk 56 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.133333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.109533 restraints weight = 31130.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 3.74
r_work: 0.3099 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3104
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3104 r_free = 0.3104    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3104
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   8507  Z= 0.221
  Angle     :  0.632   9.419  11671  Z= 0.315
  Chirality :  0.044   0.300   1389
  Planarity :  0.004   0.039   1426
  Dihedral  :  7.708  90.285   1344
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 12.98 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.26), residues: 1075
  helix:  2.09 (0.22), residues: 526
  sheet: -0.58 (0.53), residues: 114
  loop : -1.79 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 647 
 HIS   0.003   0.001   HIS B 135 
 PHE   0.027   0.002   PHE B 322 
 TYR   0.022   0.002   TYR B 570 
 ARG   0.007   0.000   ARG A 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00592 (    8)
  link_NAG-ASN         : angle       2.76527 (   24)
  link_BETA1-4         : bond        0.00262 (    1)
  link_BETA1-4         : angle       2.17734 (    3)
  hydrogen bonds       : bond        0.03885 (  463)
  hydrogen bonds       : angle       4.34492 ( 1342)
  SS BOND              : bond        0.00228 (    6)
  SS BOND              : angle       0.83465 (   12)
  covalent geometry    : bond        0.00528 ( 8492)
  covalent geometry    : angle       0.61845 (11632)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.969 
Fit side-chains
REVERT: A  159 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8205 (tt0)
REVERT: A  294 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.8029 (m-80)
REVERT: B  510 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8235 (ttp)
  outliers start: 19
  outliers final: 16
  residues processed: 76
  average time/residue: 0.1646
  time to fit residues: 19.2058
Evaluate side-chains
  80 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  294 TYR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  541 ILE
Chi-restraints excluded: chain A residue  561 VAL
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  326 THR
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain B residue  510 MET
Chi-restraints excluded: chain B residue  545 ILE
Chi-restraints excluded: chain B residue  561 VAL
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 14 optimal weight:   20.0000
   chunk 4 optimal weight:    0.0010
   chunk 87 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 106 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   overall best weight:    0.6988

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

Flipped N/Q/H residues before XYZ refinement:
** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.135993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.111824 restraints weight = 39113.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 4.52
r_work: 0.3118 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3121
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3121 r_free = 0.3121    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3121 r_free = 0.3121    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3121
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8507  Z= 0.144
  Angle     :  0.572   9.384  11671  Z= 0.284
  Chirality :  0.042   0.301   1389
  Planarity :  0.004   0.038   1426
  Dihedral  :  7.518  90.006   1344
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 14.23 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.27), residues: 1075
  helix:  2.38 (0.22), residues: 526
  sheet: -0.53 (0.53), residues: 114
  loop : -1.69 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 647 
 HIS   0.002   0.001   HIS B 135 
 PHE   0.024   0.001   PHE B 322 
 TYR   0.018   0.001   TYR B 570 
 ARG   0.007   0.000   ARG A 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00596 (    8)
  link_NAG-ASN         : angle       2.68285 (   24)
  link_BETA1-4         : bond        0.00299 (    1)
  link_BETA1-4         : angle       1.99059 (    3)
  hydrogen bonds       : bond        0.03338 (  463)
  hydrogen bonds       : angle       4.16106 ( 1342)
  SS BOND              : bond        0.00120 (    6)
  SS BOND              : angle       0.68188 (   12)
  covalent geometry    : bond        0.00339 ( 8492)
  covalent geometry    : angle       0.55836 (11632)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.924 
Fit side-chains
REVERT: A  159 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8210 (tt0)
REVERT: A  294 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.7938 (m-80)
REVERT: B  325 MET cc_start: 0.8431 (ttm) cc_final: 0.8191 (ttt)
REVERT: B  510 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8227 (ttp)
  outliers start: 16
  outliers final: 13
  residues processed: 82
  average time/residue: 0.1558
  time to fit residues: 19.4603
Evaluate side-chains
  85 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  164 SER
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  294 TYR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  561 VAL
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  510 MET
Chi-restraints excluded: chain B residue  545 ILE
Chi-restraints excluded: chain B residue  561 VAL
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 57 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 75 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 102 optimal weight:    0.9980
   chunk 14 optimal weight:   30.0000
   chunk 98 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.135750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.111700 restraints weight = 37168.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 4.34
r_work: 0.3132 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3137
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3137
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.1434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8507  Z= 0.143
  Angle     :  0.572   9.384  11671  Z= 0.283
  Chirality :  0.042   0.302   1389
  Planarity :  0.004   0.039   1426
  Dihedral  :  7.379  89.431   1344
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 13.98 %
    Favored  : 83.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.27), residues: 1075
  helix:  2.41 (0.22), residues: 526
  sheet: -0.46 (0.53), residues: 115
  loop : -1.65 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 647 
 HIS   0.002   0.001   HIS B 135 
 PHE   0.024   0.001   PHE B 322 
 TYR   0.018   0.001   TYR A 652 
 ARG   0.007   0.000   ARG A 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00587 (    8)
  link_NAG-ASN         : angle       2.66212 (   24)
  link_BETA1-4         : bond        0.00275 (    1)
  link_BETA1-4         : angle       1.98936 (    3)
  hydrogen bonds       : bond        0.03331 (  463)
  hydrogen bonds       : angle       4.12836 ( 1342)
  SS BOND              : bond        0.00123 (    6)
  SS BOND              : angle       0.68657 (   12)
  covalent geometry    : bond        0.00339 ( 8492)
  covalent geometry    : angle       0.55846 (11632)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.944 
Fit side-chains
REVERT: A  159 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8181 (tt0)
REVERT: A  294 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.8018 (m-80)
REVERT: B  325 MET cc_start: 0.8421 (ttm) cc_final: 0.8161 (ttt)
REVERT: B  510 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8216 (ttp)
  outliers start: 16
  outliers final: 13
  residues processed: 82
  average time/residue: 0.1665
  time to fit residues: 20.7859
Evaluate side-chains
  84 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  294 TYR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  541 ILE
Chi-restraints excluded: chain A residue  561 VAL
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  510 MET
Chi-restraints excluded: chain B residue  545 ILE
Chi-restraints excluded: chain B residue  561 VAL
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   chunk 101 optimal weight:    0.1980
   chunk 68 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0670
   chunk 8 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.137608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.114178 restraints weight = 31654.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 3.69
r_work: 0.3172 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3175
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3175
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8507  Z= 0.135
  Angle     :  0.562   9.354  11671  Z= 0.278
  Chirality :  0.042   0.303   1389
  Planarity :  0.004   0.038   1426
  Dihedral  :  7.243  88.636   1344
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 14.23 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.27), residues: 1075
  helix:  2.47 (0.22), residues: 526
  sheet: -0.44 (0.53), residues: 115
  loop : -1.62 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 647 
 HIS   0.002   0.001   HIS B 135 
 PHE   0.025   0.001   PHE B 322 
 TYR   0.019   0.001   TYR A 652 
 ARG   0.007   0.000   ARG A 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00593 (    8)
  link_NAG-ASN         : angle       2.62742 (   24)
  link_BETA1-4         : bond        0.00265 (    1)
  link_BETA1-4         : angle       1.92432 (    3)
  hydrogen bonds       : bond        0.03226 (  463)
  hydrogen bonds       : angle       4.05833 ( 1342)
  SS BOND              : bond        0.00120 (    6)
  SS BOND              : angle       0.66172 (   12)
  covalent geometry    : bond        0.00319 ( 8492)
  covalent geometry    : angle       0.54931 (11632)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.899 
Fit side-chains
REVERT: A  159 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8114 (tt0)
REVERT: A  294 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7951 (m-80)
REVERT: B  325 MET cc_start: 0.8388 (ttm) cc_final: 0.8149 (ttt)
REVERT: B  510 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8132 (ttp)
  outliers start: 16
  outliers final: 13
  residues processed: 79
  average time/residue: 0.1638
  time to fit residues: 19.8964
Evaluate side-chains
  83 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  294 TYR
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  561 VAL
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  510 MET
Chi-restraints excluded: chain B residue  545 ILE
Chi-restraints excluded: chain B residue  561 VAL
Chi-restraints excluded: chain B residue  584 VAL
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 106 optimal weight:    0.9980
   chunk 11 optimal weight:    0.2980
   chunk 104 optimal weight:    0.9980
   chunk 84 optimal weight:    0.7980
   chunk 80 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 103 optimal weight:    0.8980
   chunk 56 optimal weight:    4.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.135882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.112128 restraints weight = 33788.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 4.15
r_work: 0.3140 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3143
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3143 r_free = 0.3143    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3143 r_free = 0.3143    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3143
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.1462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8507  Z= 0.148
  Angle     :  0.573   9.373  11671  Z= 0.283
  Chirality :  0.042   0.303   1389
  Planarity :  0.004   0.038   1426
  Dihedral  :  7.228  88.145   1344
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 14.11 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.27), residues: 1075
  helix:  2.44 (0.22), residues: 526
  sheet: -0.40 (0.53), residues: 115
  loop : -1.63 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 647 
 HIS   0.002   0.001   HIS B 135 
 PHE   0.024   0.001   PHE B 322 
 TYR   0.018   0.001   TYR B 570 
 ARG   0.007   0.000   ARG A 379 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00591 (    8)
  link_NAG-ASN         : angle       2.63685 (   24)
  link_BETA1-4         : bond        0.00233 (    1)
  link_BETA1-4         : angle       1.93690 (    3)
  hydrogen bonds       : bond        0.03309 (  463)
  hydrogen bonds       : angle       4.07450 ( 1342)
  SS BOND              : bond        0.00126 (    6)
  SS BOND              : angle       0.66016 (   12)
  covalent geometry    : bond        0.00351 ( 8492)
  covalent geometry    : angle       0.56008 (11632)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3741.63 seconds
wall clock time: 65 minutes 45.73 seconds (3945.73 seconds total)