Starting phenix.real_space_refine
on Wed Mar 12 08:51:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rgg_19132/03_2025/8rgg_19132.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rgg_19132/03_2025/8rgg_19132.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rgg_19132/03_2025/8rgg_19132.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rgg_19132/03_2025/8rgg_19132.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rgg_19132/03_2025/8rgg_19132.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rgg_19132/03_2025/8rgg_19132.cif"
  }
  resolution = 4.0
  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=   0.002 sd=   0.017
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      21      5.16       5
     C    4787      2.51       5
     N    1401      2.21       5
     O    1470      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7679
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "B"
      Number of atoms: 2297
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2297
          Classifications: {'peptide': 286}
          Link IDs: {'PTRANS': 8, 'TRANS': 277}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 277
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 277
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 47}
          Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 52}
          Chain breaks: 1
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 151
          Unresolved non-hydrogen angles: 194
          Unresolved non-hydrogen dihedrals: 122
          Unresolved non-hydrogen chiralities: 17
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 77
    Chain: "D"
      Number of atoms: 3329
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 456, 3329
          Classifications: {'peptide': 456}
          Incomplete info: {'truncation_to_alanine': 55}
          Link IDs: {'PTRANS': 33, 'TRANS': 422}
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 212
          Unresolved non-hydrogen angles: 277
          Unresolved non-hydrogen dihedrals: 179
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 138
    Chain: "G"
      Number of atoms: 462
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 462
          Classifications: {'peptide': 93}
          Incomplete info: {'truncation_to_alanine': 87}
          Link IDs: {'PTRANS': 5, 'TRANS': 87}
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 291
          Unresolved non-hydrogen angles: 370
          Unresolved non-hydrogen dihedrals: 231
          Unresolved non-hydrogen chiralities: 33
          Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 139
    Chain: "H"
      Number of atoms: 462
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 462
          Classifications: {'peptide': 93}
          Incomplete info: {'truncation_to_alanine': 87}
          Link IDs: {'PTRANS': 5, 'TRANS': 87}
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 291
          Unresolved non-hydrogen angles: 370
          Unresolved non-hydrogen dihedrals: 231
          Unresolved non-hydrogen chiralities: 33
          Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 139
    Chain: "I"
      Number of atoms: 426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 426
          Classifications: {'peptide': 86}
          Incomplete info: {'truncation_to_alanine': 75}
          Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 83}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 296
          Unresolved non-hydrogen angles: 376
          Unresolved non-hydrogen dihedrals: 257
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 172
    Chain: "J"
      Number of atoms: 426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 426
          Classifications: {'peptide': 86}
          Incomplete info: {'truncation_to_alanine': 75}
          Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 83}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 296
          Unresolved non-hydrogen angles: 376
          Unresolved non-hydrogen dihedrals: 257
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 172
  Time building chain proxies: 4.63, per 1000 atoms: 0.60
  Number of scatterers: 7679
  At special positions: 0
  Unit cell: (87.768, 114.264, 104.328, 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      21     16.00
     O    1470      8.00
     N    1401      7.00
     C    4787      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.52
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2194

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 10 sheets defined
      41.6% alpha, 16.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'B' and resid 395 through 411
    Processing helix  chain 'B' and resid 413 through 424
    Processing helix  chain 'B' and resid 424 through 430
      removed outlier: 3.920A  pdb=" N   ARG B 430 " --> pdb=" O   GLU B 426 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 437
    Processing helix  chain 'B' and resid 437 through 463
    Processing helix  chain 'B' and resid 480 through 508
      removed outlier: 4.053A  pdb=" N   SER B 508 " --> pdb=" O   GLU B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 548
      removed outlier: 3.826A  pdb=" N   ARG B 514 " --> pdb=" O   LEU B 510 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   CYS B 515 " --> pdb=" O   PRO B 511 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ASP B 548 " --> pdb=" O   SER B 544 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 549 through 552
    Processing helix  chain 'B' and resid 576 through 593
      removed outlier: 3.579A  pdb=" N   VAL B 580 " --> pdb=" O   SER B 576 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 597 through 631
      removed outlier: 3.629A  pdb=" N   LYS B 609 " --> pdb=" O   ASN B 605 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   LYS B 612 " --> pdb=" O   GLN B 608 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   GLN B 613 " --> pdb=" O   LYS B 609 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   MET B 631 " --> pdb=" O   ILE B 627 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 632 through 634
      No H-bonds generated for 'chain 'B' and resid 632 through 634'
    Processing helix  chain 'B' and resid 635 through 653
      removed outlier: 4.638A  pdb=" N   MET B 639 " --> pdb=" O   GLN B 635 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   SER B 642 " --> pdb=" O   MET B 638 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ALA B 645 " --> pdb=" O   GLN B 641 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   PHE B 646 " --> pdb=" O   SER B 642 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ILE B 649 " --> pdb=" O   ALA B 645 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 669 through 693
      removed outlier: 3.603A  pdb=" N   ARG B 684 " --> pdb=" O   ASN B 680 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 578 through 585
      removed outlier: 3.666A  pdb=" N   ASP C 584 " --> pdb=" O   MET C 580 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 585 through 611
    Processing helix  chain 'D' and resid 99 through 103
      removed outlier: 3.880A  pdb=" N   GLN D 102 " --> pdb=" O   PRO D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 129
      removed outlier: 3.832A  pdb=" N   LEU D 108 " --> pdb=" O   ASP D 104 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ARG D 121 " --> pdb=" O   ALA D 117 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 154 through 160
      removed outlier: 3.984A  pdb=" N   GLN D 160 " --> pdb=" O   PRO D 156 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 513 through 518
    Processing helix  chain 'D' and resid 522 through 534
      removed outlier: 4.316A  pdb=" N   VAL D 534 " --> pdb=" O   LEU D 530 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 4 through 13
    Processing helix  chain 'G' and resid 35 through 61
    Processing helix  chain 'H' and resid 4 through 13
    Processing helix  chain 'H' and resid 35 through 61
    Processing helix  chain 'I' and resid 14 through 32
    Processing helix  chain 'I' and resid 34 through 50
      removed outlier: 3.661A  pdb=" N   ILE I  38 " --> pdb=" O   ILE I  34 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 14 through 32
    Processing helix  chain 'J' and resid 34 through 50
    Processing sheet with id=AA1, first strand: chain 'B' and resid 562 through 564
    Processing sheet with id=AA2, first strand: chain 'C' and resid 552 through 558
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 566 through 568
    current: chain 'I' and resid 72 through 78
      removed outlier: 6.705A  pdb=" N   HIS I  72 " --> pdb=" O   LYS I  87 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   LYS I  87 " --> pdb=" O   HIS I  72 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'I' and resid 81 through 87
    current: chain 'J' and resid 81 through 87
    Processing sheet with id=AA3, first strand: chain 'D' and resid 152 through 153
      removed outlier: 3.683A  pdb=" N   THR D 506 " --> pdb=" O   ASP D 502 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 168 through 169
      removed outlier: 3.784A  pdb=" N   PHE D 194 " --> pdb=" O   TYR D 180 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 224 through 225
      removed outlier: 3.582A  pdb=" N   TRP D 256 " --> pdb=" O   VAL D 244 " (cutoff:3.500A)
      removed outlier: 7.198A  pdb=" N   ASP D 246 " --> pdb=" O   LEU D 254 " (cutoff:3.500A)
      removed outlier: 5.349A  pdb=" N   LEU D 254 " --> pdb=" O   ASP D 246 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 269 through 276
      removed outlier: 3.666A  pdb=" N   GLN D 271 " --> pdb=" O   VAL D 289 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   VAL D 289 " --> pdb=" O   GLN D 271 " (cutoff:3.500A)
      removed outlier: 9.725A  pdb=" N   PHE D 284 " --> pdb=" O   GLY D 300 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   GLY D 300 " --> pdb=" O   PHE D 284 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ALA D 290 " --> pdb=" O   LYS D 294 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   LYS D 294 " --> pdb=" O   ALA D 290 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   VAL D 295 " --> pdb=" O   GLY D 311 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   GLY D 311 " --> pdb=" O   VAL D 295 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   LEU D 297 " --> pdb=" O   THR D 309 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 341 through 342
      removed outlier: 6.543A  pdb=" N   LYS D 361 " --> pdb=" O   GLN D 385 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 395 through 400
      removed outlier: 3.848A  pdb=" N   GLY D 412 " --> pdb=" O   HIS D 416 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   HIS D 416 " --> pdb=" O   GLY D 412 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 438 through 443
      removed outlier: 3.818A  pdb=" N   ALA D 440 " --> pdb=" O   ALA D 454 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ALA D 454 " --> pdb=" O   ALA D 440 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'G' and resid 29 through 32
      removed outlier: 6.626A  pdb=" N   VAL G  22 " --> pdb=" O   ILE G  30 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   SER G  32 " --> pdb=" O   ILE G  20 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   ILE G  20 " --> pdb=" O   SER G  32 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   THR G  67 " --> pdb=" O   PRO G  82 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   LEU G  66 " --> pdb=" O   SER H  73 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   SER H  73 " --> pdb=" O   LEU G  66 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   PHE G  68 " --> pdb=" O   ILE H  71 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   ILE H  71 " --> pdb=" O   PHE G  68 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   ARG G  70 " --> pdb=" O   LEU H  69 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   LEU H  69 " --> pdb=" O   ARG G  70 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ARG G  72 " --> pdb=" O   THR H  67 " (cutoff:3.500A)
      removed outlier: 5.714A  pdb=" N   THR H  67 " --> pdb=" O   PRO H  82 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ILE H  91 " --> pdb=" O   GLY H  19 " (cutoff:3.500A)

    465 hydrogen bonds defined for protein.
    1341 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: 2.42

  Time building geometry restraints manager: 1.83 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1934
        1.33 -     1.46: 1337
        1.46 -     1.58: 4483
        1.58 -     1.70: 0
        1.70 -     1.82: 30
  Bond restraints: 7784
  Sorted by residual:
  bond pdb=" CA  PRO D  99 "
       pdb=" C   PRO D  99 "
    ideal  model  delta    sigma   weight residual
    1.517  1.545 -0.028 6.70e-03 2.23e+04 1.75e+01
  bond pdb=" CA  LEU D 221 "
       pdb=" CB  LEU D 221 "
    ideal  model  delta    sigma   weight residual
    1.528  1.564 -0.035 1.13e-02 7.83e+03 9.78e+00
  bond pdb=" N   GLY D 501 "
       pdb=" CA  GLY D 501 "
    ideal  model  delta    sigma   weight residual
    1.444  1.474 -0.030 1.02e-02 9.61e+03 8.76e+00
  bond pdb=" CZ  ARG D 348 "
       pdb=" NH2 ARG D 348 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.30e-02 5.92e+03 8.64e+00
  bond pdb=" N   PRO D 230 "
       pdb=" CD  PRO D 230 "
    ideal  model  delta    sigma   weight residual
    1.473  1.432  0.041 1.40e-02 5.10e+03 8.45e+00
  ... (remaining 7779 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.17: 8199
        2.17 -     4.35: 2205
        4.35 -     6.52: 203
        6.52 -     8.69: 27
        8.69 -    10.87: 3
  Bond angle restraints: 10637
  Sorted by residual:
  angle pdb=" CA  PHE D 439 "
        pdb=" CB  PHE D 439 "
        pdb=" CG  PHE D 439 "
      ideal   model   delta    sigma   weight residual
     113.80  120.71   -6.91 1.00e+00 1.00e+00 4.77e+01
  angle pdb=" N   ALA J  11 "
        pdb=" CA  ALA J  11 "
        pdb=" C   ALA J  11 "
      ideal   model   delta    sigma   weight residual
     107.23  118.10  -10.87 1.67e+00 3.59e-01 4.23e+01
  angle pdb=" C   LEU D 255 "
        pdb=" N   TRP D 256 "
        pdb=" CA  TRP D 256 "
      ideal   model   delta    sigma   weight residual
     121.40  130.50   -9.10 1.52e+00 4.33e-01 3.59e+01
  angle pdb=" CA  PHE B 646 "
        pdb=" CB  PHE B 646 "
        pdb=" CG  PHE B 646 "
      ideal   model   delta    sigma   weight residual
     113.80  119.54   -5.74 1.00e+00 1.00e+00 3.30e+01
  angle pdb=" C   ARG D 206 "
        pdb=" N   PRO D 207 "
        pdb=" CA  PRO D 207 "
      ideal   model   delta    sigma   weight residual
     119.24  125.16   -5.92 1.04e+00 9.25e-01 3.24e+01
  ... (remaining 10632 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.04: 4362
       17.04 -    34.08: 268
       34.08 -    51.11: 30
       51.11 -    68.15: 14
       68.15 -    85.19: 9
  Dihedral angle restraints: 4683
    sinusoidal: 1328
      harmonic: 3355
  Sorted by residual:
  dihedral pdb=" CA  VAL G  17 "
           pdb=" C   VAL G  17 "
           pdb=" N   GLN G  18 "
           pdb=" CA  GLN G  18 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.27   29.73     0      5.00e+00 4.00e-02 3.54e+01
  dihedral pdb=" CA  LEU D 255 "
           pdb=" C   LEU D 255 "
           pdb=" N   TRP D 256 "
           pdb=" CA  TRP D 256 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.54   29.46     0      5.00e+00 4.00e-02 3.47e+01
  dihedral pdb=" CA  ALA J  11 "
           pdb=" C   ALA J  11 "
           pdb=" N   ASP J  12 "
           pdb=" CA  ASP J  12 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.77   29.23     0      5.00e+00 4.00e-02 3.42e+01
  ... (remaining 4680 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.097: 889
       0.097 -    0.195: 344
       0.195 -    0.292: 48
       0.292 -    0.390: 5
       0.390 -    0.487: 4
  Chirality restraints: 1290
  Sorted by residual:
  chirality pdb=" CA  THR D 309 "
            pdb=" N   THR D 309 "
            pdb=" C   THR D 309 "
            pdb=" CB  THR D 309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.04    0.49 2.00e-01 2.50e+01 5.93e+00
  chirality pdb=" CA  THR G  25 "
            pdb=" N   THR G  25 "
            pdb=" C   THR G  25 "
            pdb=" CB  THR G  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.07    0.46 2.00e-01 2.50e+01 5.30e+00
  chirality pdb=" CA  SER D 239 "
            pdb=" N   SER D 239 "
            pdb=" C   SER D 239 "
            pdb=" CB  SER D 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.21e+00
  ... (remaining 1287 not shown)

  Planarity restraints: 1422
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 169 "   -0.134 2.00e-02 2.50e+03   7.20e-02 1.30e+02
        pdb=" CG  TRP D 169 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 169 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 169 "    0.083 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 169 "    0.046 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 169 "    0.022 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 169 "    0.100 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 169 "   -0.080 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 169 "    0.015 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 169 "   -0.085 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 674 "    0.124 2.00e-02 2.50e+03   6.36e-02 8.09e+01
        pdb=" CG  TYR B 674 "   -0.064 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 674 "   -0.048 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 674 "   -0.055 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 674 "   -0.024 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 674 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 674 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B 674 "    0.081 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 298 "   -0.106 2.00e-02 2.50e+03   5.37e-02 7.20e+01
        pdb=" CG  TRP D 298 "    0.017 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 298 "    0.039 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 298 "    0.048 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 298 "    0.031 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 298 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 298 "    0.063 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 298 "   -0.073 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 298 "    0.029 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 298 "   -0.048 2.00e-02 2.50e+03
  ... (remaining 1419 not shown)

  Histogram of nonbonded interaction distances:
        2.53 -     3.00: 3607
        3.00 -     3.48: 7741
        3.48 -     3.95: 11763
        3.95 -     4.43: 12276
        4.43 -     4.90: 21375
  Nonbonded interactions: 56762
  Sorted by model distance:
  nonbonded pdb=" OG  SER D 231 "
            pdb=" OD1 ASP D 246 "
     model   vdw
     2.531 3.040
  nonbonded pdb=" OD1 ASP D 246 "
            pdb=" OG  SER D 248 "
     model   vdw
     2.547 3.040
  nonbonded pdb=" OG  SER B 549 "
            pdb=" OE2 GLU B 556 "
     model   vdw
     2.548 3.040
  nonbonded pdb=" OG  SER B 642 "
            pdb=" OE1 GLU B 688 "
     model   vdw
     2.549 3.040
  nonbonded pdb=" OD1 ASP D 263 "
            pdb=" OG  SER D 377 "
     model   vdw
     2.569 3.040
  ... (remaining 56757 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 'G'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'I'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.900
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.250
  Find NCS groups from input model:        0.120
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4596
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      :  0.012   0.041   7784  Z= 0.819
  Angle     :  1.849  10.868  10637  Z= 1.270
  Chirality :  0.099   0.487   1290
  Planarity :  0.014   0.191   1422
  Dihedral  : 13.181  85.189   2489
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 0.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Cbeta Deviations :  0.46 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.18 %
    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: -0.27 (0.22), residues: 1138
  helix:  0.44 (0.22), residues: 414
  sheet:  0.59 (0.31), residues: 189
  loop : -0.91 (0.26), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.134   0.029   TRP D 169 
 HIS   0.016   0.005   HIS D 404 
 PHE   0.090   0.012   PHE D 350 
 TYR   0.124   0.014   TYR B 674 
 ARG   0.009   0.001   ARG B 636 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  577 ASP cc_start: 0.4181 (m-30) cc_final: 0.3816 (p0)
REVERT: B  613 GLN cc_start: 0.7368 (mt0) cc_final: 0.6724 (mp10)
REVERT: D  198 TRP cc_start: 0.6589 (m-90) cc_final: 0.6038 (m100)
REVERT: D  374 MET cc_start: 0.2478 (mmm) cc_final: 0.1430 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.2155
  time to fit residues: 42.2474
Evaluate side-chains
  74 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 84 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   chunk 28 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   chunk 45 optimal weight:   10.0000
   chunk 87 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 101 optimal weight:    7.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 534 GLN
** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 285 GLN
D 418 HIS
** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 494 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.110434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.097996 restraints weight = 40213.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.097981 restraints weight = 31840.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.098703 restraints weight = 28634.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.4060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5526
moved from start:          0.3736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7784  Z= 0.238
  Angle     :  0.709   9.814  10637  Z= 0.388
  Chirality :  0.047   0.156   1290
  Planarity :  0.004   0.040   1422
  Dihedral  :  5.936  27.277   1195
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 10.43 %
    Favored  : 87.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.18 %
    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:  0.71 (0.24), residues: 1138
  helix:  1.74 (0.23), residues: 422
  sheet: -0.02 (0.30), residues: 241
  loop : -0.35 (0.30), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP D 298 
 HIS   0.005   0.002   HIS B 622 
 PHE   0.028   0.003   PHE B 646 
 TYR   0.026   0.002   TYR B 674 
 ARG   0.004   0.001   ARG B 447 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  435 LYS cc_start: 0.8202 (mptt) cc_final: 0.7821 (pttt)
REVERT: B  577 ASP cc_start: 0.6460 (m-30) cc_final: 0.5810 (p0)
REVERT: B  649 ILE cc_start: 0.7211 (mt) cc_final: 0.6880 (tt)
REVERT: B  674 TYR cc_start: 0.1784 (t80) cc_final: 0.1492 (t80)
REVERT: D  145 MET cc_start: 0.8405 (mmm) cc_final: 0.8062 (mmm)
REVERT: D  241 GLU cc_start: 0.6474 (tt0) cc_final: 0.6148 (tp30)
  outliers start: 13
  outliers final: 8
  residues processed: 91
  average time/residue: 0.1992
  time to fit residues: 24.9506
Evaluate side-chains
  73 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  534 GLN
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain D residue  192 LYS
Chi-restraints excluded: chain D residue  263 ASP
Chi-restraints excluded: chain D residue  408 PHE
Chi-restraints excluded: chain D residue  438 LEU
Chi-restraints excluded: chain D residue  451 PHE
Chi-restraints excluded: chain D residue  507 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 17 optimal weight:    0.0370
   chunk 91 optimal weight:    1.9990
   chunk 8 optimal weight:    8.9990
   chunk 49 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0670
   chunk 47 optimal weight:   10.0000
   chunk 83 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9990
   chunk 60 optimal weight:   10.0000
   chunk 76 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    0.8000

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

Flipped N/Q/H residues before XYZ refinement:
** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 461 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 = 0.4312 r_free = 0.4312 target = 0.110771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.098339 restraints weight = 41145.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.099199 restraints weight = 34846.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.099796 restraints weight = 27575.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.4086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5464
moved from start:          0.4342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7784  Z= 0.161
  Angle     :  0.600   9.782  10637  Z= 0.320
  Chirality :  0.044   0.131   1290
  Planarity :  0.003   0.033   1422
  Dihedral  :  5.214  26.608   1195
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 11.79 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.25), residues: 1138
  helix:  2.27 (0.24), residues: 429
  sheet:  0.10 (0.32), residues: 222
  loop : -0.33 (0.30), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP D 198 
 HIS   0.009   0.001   HIS B 574 
 PHE   0.019   0.002   PHE D 408 
 TYR   0.025   0.002   TYR D 486 
 ARG   0.004   0.000   ARG B 514 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  562 MET cc_start: 0.3510 (ptt) cc_final: 0.2541 (ptt)
REVERT: B  649 ILE cc_start: 0.7501 (mt) cc_final: 0.7040 (tt)
REVERT: B  674 TYR cc_start: 0.1577 (t80) cc_final: 0.1279 (t80)
REVERT: D  256 TRP cc_start: 0.6041 (OUTLIER) cc_final: 0.5735 (m-10)
REVERT: D  386 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7556 (t80)
REVERT: D  422 MET cc_start: 0.6134 (mtt) cc_final: 0.5271 (mmt)
  outliers start: 16
  outliers final: 7
  residues processed: 78
  average time/residue: 0.1724
  time to fit residues: 19.3036
Evaluate side-chains
  67 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain D residue  192 LYS
Chi-restraints excluded: chain D residue  256 TRP
Chi-restraints excluded: chain D residue  386 PHE
Chi-restraints excluded: chain D residue  498 LEU
Chi-restraints excluded: chain D residue  506 THR
Chi-restraints excluded: chain D residue  507 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 19 optimal weight:    0.0980
   chunk 110 optimal weight:    0.1980
   chunk 11 optimal weight:    2.9990
   chunk 36 optimal weight:   20.0000
   chunk 13 optimal weight:    5.9990
   chunk 73 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   chunk 74 optimal weight:    1.9990
   chunk 31 optimal weight:    8.9990
   chunk 33 optimal weight:   20.0000
   chunk 24 optimal weight:    9.9990
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 630 GLN
D 163 HIS
** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.107579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.095075 restraints weight = 40718.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.095185 restraints weight = 36353.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.095905 restraints weight = 32273.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.4013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5673
moved from start:          0.5139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7784  Z= 0.221
  Angle     :  0.636   9.184  10637  Z= 0.341
  Chirality :  0.045   0.182   1290
  Planarity :  0.004   0.035   1422
  Dihedral  :  5.198  26.037   1195
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 12.99 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.18 %
    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:  0.87 (0.25), residues: 1138
  helix:  2.08 (0.24), residues: 428
  sheet:  0.14 (0.33), residues: 221
  loop : -0.53 (0.29), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP D 198 
 HIS   0.006   0.001   HIS B 574 
 PHE   0.019   0.002   PHE B 516 
 TYR   0.031   0.002   TYR D 486 
 ARG   0.004   0.001   ARG D 206 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  562 MET cc_start: 0.3975 (ptt) cc_final: 0.2992 (ptt)
REVERT: B  649 ILE cc_start: 0.7309 (mt) cc_final: 0.6995 (tt)
REVERT: D  241 GLU cc_start: 0.5665 (tp30) cc_final: 0.5450 (tp30)
REVERT: D  256 TRP cc_start: 0.6263 (OUTLIER) cc_final: 0.5975 (m-10)
REVERT: D  386 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7729 (t80)
REVERT: D  422 MET cc_start: 0.6690 (mtt) cc_final: 0.5590 (mmt)
  outliers start: 21
  outliers final: 15
  residues processed: 78
  average time/residue: 0.1570
  time to fit residues: 18.2829
Evaluate side-chains
  72 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 55
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  256 TRP
Chi-restraints excluded: chain D residue  263 ASP
Chi-restraints excluded: chain D residue  386 PHE
Chi-restraints excluded: chain D residue  408 PHE
Chi-restraints excluded: chain D residue  438 LEU
Chi-restraints excluded: chain D residue  455 SER
Chi-restraints excluded: chain D residue  465 LEU
Chi-restraints excluded: chain D residue  475 LEU
Chi-restraints excluded: chain D residue  498 LEU
Chi-restraints excluded: chain D residue  506 THR
Chi-restraints excluded: chain D residue  507 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 28 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 60 optimal weight:    0.9980
   chunk 76 optimal weight:    0.0770
   chunk 24 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 94 optimal weight:   20.0000
   overall best weight:    2.4144

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

Flipped N/Q/H residues before XYZ refinement:
** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 461 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 = 0.4230 r_free = 0.4230 target = 0.105809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.093494 restraints weight = 40794.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.093401 restraints weight = 38181.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.094152 restraints weight = 32222.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5756
moved from start:          0.5868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7784  Z= 0.216
  Angle     :  0.633   8.305  10637  Z= 0.337
  Chirality :  0.045   0.187   1290
  Planarity :  0.004   0.039   1422
  Dihedral  :  5.262  27.053   1195
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 13.85 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.18 %
    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:  0.71 (0.25), residues: 1138
  helix:  1.97 (0.24), residues: 428
  sheet: -0.02 (0.32), residues: 227
  loop : -0.63 (0.30), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D 245 
 HIS   0.006   0.001   HIS B 574 
 PHE   0.020   0.002   PHE D 350 
 TYR   0.031   0.002   TYR D 486 
 ARG   0.017   0.001   ARG B 447 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 59
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  447 ARG cc_start: 0.7663 (mtt180) cc_final: 0.7185 (ttt180)
REVERT: D  241 GLU cc_start: 0.5878 (tp30) cc_final: 0.5600 (tp30)
REVERT: D  386 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7763 (t80)
REVERT: D  463 PHE cc_start: 0.6801 (t80) cc_final: 0.6513 (t80)
  outliers start: 24
  outliers final: 16
  residues processed: 75
  average time/residue: 0.1498
  time to fit residues: 17.2087
Evaluate side-chains
  71 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain B residue  650 ILE
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  263 ASP
Chi-restraints excluded: chain D residue  386 PHE
Chi-restraints excluded: chain D residue  408 PHE
Chi-restraints excluded: chain D residue  446 VAL
Chi-restraints excluded: chain D residue  455 SER
Chi-restraints excluded: chain D residue  465 LEU
Chi-restraints excluded: chain D residue  475 LEU
Chi-restraints excluded: chain D residue  498 LEU
Chi-restraints excluded: chain D residue  506 THR
Chi-restraints excluded: chain D residue  507 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 39 optimal weight:    0.2980
   chunk 95 optimal weight:   10.0000
   chunk 85 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 74 optimal weight:    9.9990
   chunk 97 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 89 optimal weight:   20.0000
   chunk 106 optimal weight:    5.9990
   chunk 15 optimal weight:    8.9990
   overall best weight:    3.2186

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

Flipped N/Q/H residues before XYZ refinement:
B 605 ASN
B 652 ASN
** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.103826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.091786 restraints weight = 40665.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.091931 restraints weight = 33218.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.092351 restraints weight = 33624.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5876
moved from start:          0.6588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7784  Z= 0.260
  Angle     :  0.683   8.681  10637  Z= 0.363
  Chirality :  0.046   0.211   1290
  Planarity :  0.004   0.039   1422
  Dihedral  :  5.553  28.135   1195
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 14.02 %
    Favored  : 81.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.25), residues: 1138
  helix:  1.53 (0.24), residues: 428
  sheet: -0.44 (0.31), residues: 230
  loop : -0.86 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D 245 
 HIS   0.005   0.001   HIS B 574 
 PHE   0.017   0.003   PHE B 535 
 TYR   0.037   0.003   TYR D 486 
 ARG   0.005   0.001   ARG B 584 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 57
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  404 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7541 (tptp)
REVERT: B  447 ARG cc_start: 0.7756 (mtt180) cc_final: 0.7219 (ttt180)
REVERT: B  535 PHE cc_start: 0.4762 (OUTLIER) cc_final: 0.3716 (t80)
REVERT: D  386 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7964 (t80)
REVERT: D  439 PHE cc_start: 0.4127 (OUTLIER) cc_final: 0.3145 (p90)
REVERT: D  463 PHE cc_start: 0.6986 (t80) cc_final: 0.6685 (t80)
  outliers start: 28
  outliers final: 18
  residues processed: 77
  average time/residue: 0.1653
  time to fit residues: 18.9734
Evaluate side-chains
  77 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 55
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  404 LYS
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  535 PHE
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain B residue  650 ILE
Chi-restraints excluded: chain D residue  183 LEU
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  231 SER
Chi-restraints excluded: chain D residue  263 ASP
Chi-restraints excluded: chain D residue  386 PHE
Chi-restraints excluded: chain D residue  439 PHE
Chi-restraints excluded: chain D residue  446 VAL
Chi-restraints excluded: chain D residue  451 PHE
Chi-restraints excluded: chain D residue  455 SER
Chi-restraints excluded: chain D residue  475 LEU
Chi-restraints excluded: chain D residue  486 TYR
Chi-restraints excluded: chain D residue  498 LEU
Chi-restraints excluded: chain D residue  506 THR
Chi-restraints excluded: chain D residue  507 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 78 optimal weight:    5.9990
   chunk 79 optimal weight:   20.0000
   chunk 12 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 40 optimal weight:    0.2980
   chunk 23 optimal weight:    0.5980
   chunk 57 optimal weight:    6.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
D 424 GLN
** D 461 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 = 0.4252 r_free = 0.4252 target = 0.106573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.094000 restraints weight = 40398.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.093945 restraints weight = 36001.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.094732 restraints weight = 30947.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5734
moved from start:          0.6535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7784  Z= 0.142
  Angle     :  0.584  12.472  10637  Z= 0.302
  Chirality :  0.044   0.207   1290
  Planarity :  0.004   0.040   1422
  Dihedral  :  4.844  25.786   1195
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 16.24 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.18 %
    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:  0.80 (0.26), residues: 1138
  helix:  2.32 (0.25), residues: 429
  sheet: -0.26 (0.32), residues: 230
  loop : -0.72 (0.30), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 245 
 HIS   0.007   0.001   HIS D 265 
 PHE   0.017   0.002   PHE D 408 
 TYR   0.018   0.002   TYR D 486 
 ARG   0.004   0.001   ARG B 584 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  447 ARG cc_start: 0.7649 (mtt180) cc_final: 0.7119 (ttt180)
REVERT: B  535 PHE cc_start: 0.4587 (OUTLIER) cc_final: 0.4101 (t80)
REVERT: B  639 MET cc_start: 0.5357 (OUTLIER) cc_final: 0.5123 (tpp)
REVERT: D  205 LEU cc_start: 0.7964 (tp) cc_final: 0.7626 (pt)
REVERT: D  271 GLN cc_start: 0.7170 (tp-100) cc_final: 0.6663 (tp-100)
REVERT: D  386 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7753 (t80)
REVERT: D  439 PHE cc_start: 0.3532 (OUTLIER) cc_final: 0.2810 (p90)
REVERT: D  463 PHE cc_start: 0.6809 (t80) cc_final: 0.6570 (t80)
  outliers start: 19
  outliers final: 9
  residues processed: 80
  average time/residue: 0.1786
  time to fit residues: 20.4228
Evaluate side-chains
  68 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  535 PHE
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain D residue  183 LEU
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  263 ASP
Chi-restraints excluded: chain D residue  386 PHE
Chi-restraints excluded: chain D residue  438 LEU
Chi-restraints excluded: chain D residue  439 PHE
Chi-restraints excluded: chain D residue  446 VAL
Chi-restraints excluded: chain D residue  486 TYR
Chi-restraints excluded: chain D residue  506 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 100 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 81 optimal weight:    9.9990
   chunk 47 optimal weight:    4.9990
   chunk 102 optimal weight:   30.0000
   chunk 80 optimal weight:   10.0000
   chunk 82 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0170
   chunk 68 optimal weight:    2.9990
   overall best weight:    3.0026

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

Flipped N/Q/H residues before XYZ refinement:
** D 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 470 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 = 0.4202 r_free = 0.4202 target = 0.103890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.091820 restraints weight = 41034.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.092017 restraints weight = 34355.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.092495 restraints weight = 32463.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5889
moved from start:          0.6977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7784  Z= 0.241
  Angle     :  0.660  12.043  10637  Z= 0.349
  Chirality :  0.045   0.140   1290
  Planarity :  0.004   0.042   1422
  Dihedral  :  5.259  27.045   1195
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 15.90 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.18 %
    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:  0.28 (0.25), residues: 1138
  helix:  1.87 (0.25), residues: 430
  sheet: -0.74 (0.32), residues: 233
  loop : -0.86 (0.30), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D 245 
 HIS   0.005   0.001   HIS B 574 
 PHE   0.018   0.002   PHE D 350 
 TYR   0.025   0.002   TYR D 486 
 ARG   0.005   0.001   ARG B 584 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 56
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
REVERT: B  447 ARG cc_start: 0.7730 (mtt180) cc_final: 0.7166 (ttt180)
REVERT: B  535 PHE cc_start: 0.4694 (OUTLIER) cc_final: 0.3905 (t80)
REVERT: D  241 GLU cc_start: 0.5802 (tp30) cc_final: 0.5581 (tp30)
REVERT: D  256 TRP cc_start: 0.6293 (OUTLIER) cc_final: 0.6009 (m-10)
REVERT: D  271 GLN cc_start: 0.7484 (tp-100) cc_final: 0.7249 (tp-100)
REVERT: D  386 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7934 (t80)
REVERT: D  439 PHE cc_start: 0.4340 (OUTLIER) cc_final: 0.3260 (p90)
REVERT: D  463 PHE cc_start: 0.7034 (t80) cc_final: 0.6641 (t80)
  outliers start: 23
  outliers final: 15
  residues processed: 73
  average time/residue: 0.1753
  time to fit residues: 18.5784
Evaluate side-chains
  73 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 54
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  535 PHE
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain D residue  183 LEU
Chi-restraints excluded: chain D residue  215 GLU
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  256 TRP
Chi-restraints excluded: chain D residue  263 ASP
Chi-restraints excluded: chain D residue  386 PHE
Chi-restraints excluded: chain D residue  438 LEU
Chi-restraints excluded: chain D residue  439 PHE
Chi-restraints excluded: chain D residue  446 VAL
Chi-restraints excluded: chain D residue  451 PHE
Chi-restraints excluded: chain D residue  486 TYR
Chi-restraints excluded: chain D residue  498 LEU
Chi-restraints excluded: chain D residue  506 THR
Chi-restraints excluded: chain D residue  507 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 73 optimal weight:    7.9990
   chunk 107 optimal weight:    5.9990
   chunk 82 optimal weight:   20.0000
   chunk 59 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 79 optimal weight:    9.9990
   chunk 84 optimal weight:    0.6980
   chunk 92 optimal weight:    8.9990
   chunk 24 optimal weight:    0.9980
   chunk 69 optimal weight:    8.9990
   chunk 75 optimal weight:    0.5980
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
** D 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 470 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.104980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.092487 restraints weight = 40889.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.092660 restraints weight = 32272.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.093133 restraints weight = 29013.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5851
moved from start:          0.7080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7784  Z= 0.176
  Angle     :  0.622  11.999  10637  Z= 0.318
  Chirality :  0.044   0.185   1290
  Planarity :  0.004   0.039   1422
  Dihedral  :  4.995  25.559   1195
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 16.58 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.18 %
    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:  0.44 (0.26), residues: 1138
  helix:  2.13 (0.25), residues: 430
  sheet: -0.81 (0.32), residues: 239
  loop : -0.82 (0.30), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 245 
 HIS   0.004   0.001   HIS B 574 
 PHE   0.018   0.002   PHE D 350 
 TYR   0.014   0.002   TYR D 486 
 ARG   0.002   0.000   ARG B 587 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 52
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
REVERT: B  447 ARG cc_start: 0.7682 (mtt180) cc_final: 0.7101 (ttt180)
REVERT: B  535 PHE cc_start: 0.4523 (OUTLIER) cc_final: 0.4072 (t80)
REVERT: D  241 GLU cc_start: 0.5706 (tp30) cc_final: 0.5480 (tp30)
REVERT: D  256 TRP cc_start: 0.6205 (OUTLIER) cc_final: 0.5988 (m-10)
REVERT: D  386 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7888 (t80)
REVERT: D  439 PHE cc_start: 0.4049 (OUTLIER) cc_final: 0.2987 (p90)
REVERT: D  463 PHE cc_start: 0.6974 (t80) cc_final: 0.6693 (t80)
  outliers start: 21
  outliers final: 14
  residues processed: 67
  average time/residue: 0.1636
  time to fit residues: 16.6499
Evaluate side-chains
  67 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 49
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  535 PHE
Chi-restraints excluded: chain D residue  183 LEU
Chi-restraints excluded: chain D residue  215 GLU
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  256 TRP
Chi-restraints excluded: chain D residue  263 ASP
Chi-restraints excluded: chain D residue  386 PHE
Chi-restraints excluded: chain D residue  438 LEU
Chi-restraints excluded: chain D residue  439 PHE
Chi-restraints excluded: chain D residue  446 VAL
Chi-restraints excluded: chain D residue  451 PHE
Chi-restraints excluded: chain D residue  486 TYR
Chi-restraints excluded: chain D residue  498 LEU
Chi-restraints excluded: chain D residue  506 THR
Chi-restraints excluded: chain D residue  507 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 34 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   chunk 32 optimal weight:    7.9990
   chunk 83 optimal weight:    9.9990
   chunk 24 optimal weight:    6.9990
   chunk 8 optimal weight:    0.0670
   chunk 94 optimal weight:    0.0010
   chunk 35 optimal weight:    0.5980
   chunk 106 optimal weight:    4.9990
   chunk 98 optimal weight:   20.0000
   overall best weight:    1.5328

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

Flipped N/Q/H residues before XYZ refinement:
** D 461 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 = 0.4229 r_free = 0.4229 target = 0.105135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.092878 restraints weight = 40753.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.092943 restraints weight = 34323.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.093523 restraints weight = 32690.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5836
moved from start:          0.7252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7784  Z= 0.173
  Angle     :  0.619  11.893  10637  Z= 0.314
  Chirality :  0.044   0.191   1290
  Planarity :  0.004   0.044   1422
  Dihedral  :  4.882  24.677   1195
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 17.26 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.18 %
    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:  0.50 (0.26), residues: 1138
  helix:  2.25 (0.25), residues: 430
  sheet: -0.90 (0.32), residues: 237
  loop : -0.79 (0.31), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 245 
 HIS   0.004   0.001   HIS B 574 
 PHE   0.017   0.002   PHE D 350 
 TYR   0.012   0.002   TYR D 486 
 ARG   0.012   0.001   ARG D 447 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 54
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
REVERT: B  447 ARG cc_start: 0.7704 (mtt180) cc_final: 0.7172 (ttt180)
REVERT: B  535 PHE cc_start: 0.4381 (OUTLIER) cc_final: 0.3992 (t80)
REVERT: D  241 GLU cc_start: 0.5740 (tp30) cc_final: 0.5503 (tp30)
REVERT: D  271 GLN cc_start: 0.7388 (tp-100) cc_final: 0.7126 (tp-100)
REVERT: D  386 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7902 (t80)
REVERT: D  439 PHE cc_start: 0.3958 (OUTLIER) cc_final: 0.2876 (p90)
REVERT: D  463 PHE cc_start: 0.7030 (t80) cc_final: 0.6697 (t80)
  outliers start: 20
  outliers final: 15
  residues processed: 68
  average time/residue: 0.1456
  time to fit residues: 15.4550
Evaluate side-chains
  70 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 52
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  535 PHE
Chi-restraints excluded: chain D residue  183 LEU
Chi-restraints excluded: chain D residue  215 GLU
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  263 ASP
Chi-restraints excluded: chain D residue  386 PHE
Chi-restraints excluded: chain D residue  408 PHE
Chi-restraints excluded: chain D residue  438 LEU
Chi-restraints excluded: chain D residue  439 PHE
Chi-restraints excluded: chain D residue  446 VAL
Chi-restraints excluded: chain D residue  475 LEU
Chi-restraints excluded: chain D residue  486 TYR
Chi-restraints excluded: chain D residue  498 LEU
Chi-restraints excluded: chain D residue  506 THR
Chi-restraints excluded: chain D residue  507 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 41 optimal weight:    8.9990
   chunk 88 optimal weight:    9.9990
   chunk 68 optimal weight:    6.9990
   chunk 98 optimal weight:   20.0000
   chunk 17 optimal weight:    7.9990
   chunk 47 optimal weight:    5.9990
   chunk 73 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 588 GLN
** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 209 GLN
** D 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.101981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.090042 restraints weight = 40934.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.090328 restraints weight = 33013.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.090994 restraints weight = 28962.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5996
moved from start:          0.7874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   7784  Z= 0.317
  Angle     :  0.768  12.015  10637  Z= 0.404
  Chirality :  0.047   0.138   1290
  Planarity :  0.005   0.047   1422
  Dihedral  :  5.865  32.606   1195
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 17.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 16.41 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.39 (0.26), residues: 1138
  helix:  1.32 (0.25), residues: 429
  sheet: -1.17 (0.32), residues: 233
  loop : -1.20 (0.30), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP D 245 
 HIS   0.007   0.002   HIS D 163 
 PHE   0.023   0.003   PHE D 350 
 TYR   0.037   0.003   TYR D 437 
 ARG   0.013   0.001   ARG D 447 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2172.96 seconds
wall clock time: 38 minutes 33.18 seconds (2313.18 seconds total)