Starting phenix.real_space_refine
on Fri Aug 22 20:16:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rgg_19132/08_2025/8rgg_19132.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rgg_19132/08_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_19132/08_2025/8rgg_19132.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rgg_19132/08_2025/8rgg_19132.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rgg_19132/08_2025/8rgg_19132.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rgg_19132/08_2025/8rgg_19132.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 4, 'GLU:plan': 5, 'TRP:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1}
          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: {'ASN:plan1': 4, 'HIS:plan': 2, 'ASP:plan': 3, 'GLN:plan1': 6, 'GLU:plan': 5, 'TYR:plan': 1, 'ARG:plan': 4, 'PHE:plan': 3, 'TRP: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: {'GLU:plan': 5, 'ARG:plan': 5, 'GLN:plan1': 6, 'ASN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3}
          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: {'GLU:plan': 5, 'ARG:plan': 5, 'GLN:plan1': 6, 'ASN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3}
          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: {'ARG:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 7, 'GLN:plan1': 4, 'TYR:plan': 5, 'HIS:plan': 4, 'PHE:plan': 5, 'TRP:plan': 1}
          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: {'ARG:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 7, 'GLN:plan1': 4, 'TYR:plan': 5, 'HIS:plan': 4, 'PHE:plan': 5, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 172
  Time building chain proxies: 2.05, per 1000 atoms: 0.27
  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: 0.58
  Conformation dependent library (CDL) restraints added in 522.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.29
  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: 1.23

  Time building geometry restraints manager: 0.80 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:             1.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.940
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.120
-------------------------------------------------------------------------------
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= 0.804
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.27 (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
 ARG   0.009   0.001   ARG B 636 
 TYR   0.124   0.014   TYR B 674 
 PHE   0.090   0.012   PHE D 350 
 TRP   0.134   0.029   TRP D 169 
 HIS   0.016   0.005   HIS D 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.01224 ( 7784)
  covalent geometry    : angle       1.84861 (10637)
  hydrogen bonds       : bond        0.16849 (  465)
  hydrogen bonds       : angle       6.57091 ( 1341)

*********************** 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  : 0.325 
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: 0.6725 (mp10)
REVERT: D  198 TRP cc_start: 0.6589 (m-90) cc_final: 0.6036 (m100)
REVERT: D  374 MET cc_start: 0.2478 (mmm) cc_final: 0.1429 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.0971
  time to fit residues: 19.2011
Evaluate side-chains
  73 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0980
   chunk 51 optimal weight:    0.0470
   chunk 100 optimal weight:    0.0370
   chunk 106 optimal weight:   10.0000
   overall best weight:    0.6360

-------------------------------------------------------------------------------
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 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 143 GLN
** D 226 HIS ** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.114029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.101622 restraints weight = 40309.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.101929 restraints weight = 35643.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.102587 restraints weight = 29692.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.103214 restraints weight = 23312.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.103365 restraints weight = 20766.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.4150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5289
moved from start:          0.3390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7784  Z= 0.144
  Angle     :  0.666   9.587  10637  Z= 0.364
  Chirality :  0.046   0.172   1290
  Planarity :  0.004   0.035   1422
  Dihedral  :  5.715  25.442   1195
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 10.09 %
    Favored  : 88.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.24), residues: 1138
  helix:  2.02 (0.23), residues: 426
  sheet:  0.03 (0.31), residues: 227
  loop : -0.51 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 206 
 TYR   0.024   0.002   TYR B 674 
 PHE   0.027   0.003   PHE B 646 
 TRP   0.023   0.003   TRP D 298 
 HIS   0.005   0.001   HIS B 622 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7784)
  covalent geometry    : angle       0.66621 (10637)
  hydrogen bonds       : bond        0.05097 (  465)
  hydrogen bonds       : angle       4.70634 ( 1341)

*********************** 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
  97 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.315 
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: symmetry clash
REVERT: B  435 LYS cc_start: 0.8203 (mptt) cc_final: 0.7884 (pttt)
REVERT: B  577 ASP cc_start: 0.5749 (m-30) cc_final: 0.4773 (p0)
REVERT: D  145 MET cc_start: 0.8169 (mmm) cc_final: 0.7758 (mmm)
REVERT: D  241 GLU cc_start: 0.6369 (tt0) cc_final: 0.6036 (tp30)
REVERT: D  351 ILE cc_start: 0.8569 (mm) cc_final: 0.8240 (mt)
REVERT: D  368 GLU cc_start: 0.6551 (pm20) cc_final: 0.6316 (pm20)
  outliers start: 11
  outliers final: 7
  residues processed: 93
  average time/residue: 0.0905
  time to fit residues: 11.6880
Evaluate side-chains
  73 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  444 LEU
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  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 6 optimal weight:   10.0000
   chunk 99 optimal weight:    0.7980
   chunk 24 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 63 optimal weight:    8.9990
   chunk 108 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 20 optimal weight:    0.0270
   chunk 13 optimal weight:    7.9990
   chunk 66 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    1.3040

-------------------------------------------------------------------------------
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 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 285 GLN
D 418 HIS
D 424 GLN
** D 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 470 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.111064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.098167 restraints weight = 40179.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.098444 restraints weight = 32663.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.099084 restraints weight = 26556.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.099404 restraints weight = 22528.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.099501 restraints weight = 21082.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5477
moved from start:          0.4268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7784  Z= 0.131
  Angle     :  0.602   8.236  10637  Z= 0.321
  Chirality :  0.044   0.135   1290
  Planarity :  0.004   0.034   1422
  Dihedral  :  5.079  25.375   1195
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 10.94 %
    Favored  : 85.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.22 (0.25), residues: 1138
  helix:  2.43 (0.24), residues: 431
  sheet:  0.21 (0.32), residues: 225
  loop : -0.36 (0.30), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 283 
 TYR   0.025   0.002   TYR D 486 
 PHE   0.037   0.002   PHE D 439 
 TRP   0.020   0.002   TRP D 198 
 HIS   0.009   0.001   HIS D 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 7784)
  covalent geometry    : angle       0.60172 (10637)
  hydrogen bonds       : bond        0.04441 (  465)
  hydrogen bonds       : angle       4.37841 ( 1341)

*********************** 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
  86 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  198 TRP cc_start: 0.6415 (m-90) cc_final: 0.6160 (m100)
REVERT: D  256 TRP cc_start: 0.5948 (OUTLIER) cc_final: 0.5681 (m-10)
  outliers start: 18
  outliers final: 11
  residues processed: 81
  average time/residue: 0.0771
  time to fit residues: 9.2643
Evaluate side-chains
  69 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
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  497 ASP
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain D residue  256 TRP
Chi-restraints excluded: chain D residue  263 ASP
Chi-restraints excluded: chain D residue  408 PHE
Chi-restraints excluded: chain D residue  455 SER
Chi-restraints excluded: chain D residue  465 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    9.9990
   chunk 100 optimal weight:    5.9990
   chunk 26 optimal weight:    9.9990
   chunk 39 optimal weight:    9.9990
   chunk 2 optimal weight:    0.9980
   chunk 28 optimal weight:   20.0000
   chunk 20 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 45 optimal weight:   10.0000
   chunk 61 optimal weight:    8.9990
   chunk 85 optimal weight:    8.9990
   overall best weight:    4.1986

-------------------------------------------------------------------------------
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 163 HIS
** 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 = 0.4204 r_free = 0.4204 target = 0.104366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.092345 restraints weight = 41915.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.092731 restraints weight = 35238.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.093230 restraints weight = 32195.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.093292 restraints weight = 25656.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.093499 restraints weight = 23974.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5793
moved from start:          0.5546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   7784  Z= 0.251
  Angle     :  0.765   9.451  10637  Z= 0.412
  Chirality :  0.048   0.154   1290
  Planarity :  0.005   0.046   1422
  Dihedral  :  5.861  28.978   1195
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 12.99 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.25), residues: 1138
  helix:  1.42 (0.24), residues: 428
  sheet:  0.31 (0.33), residues: 216
  loop : -0.60 (0.30), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 283 
 TYR   0.030   0.003   TYR D 486 
 PHE   0.034   0.004   PHE D 439 
 TRP   0.021   0.003   TRP D 245 
 HIS   0.008   0.002   HIS B 574 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 7784)
  covalent geometry    : angle       0.76462 (10637)
  hydrogen bonds       : bond        0.05209 (  465)
  hydrogen bonds       : angle       5.31765 ( 1341)

*********************** 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
  84 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 62
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  198 TRP cc_start: 0.6658 (m-90) cc_final: 0.6250 (m100)
REVERT: D  386 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7856 (t80)
REVERT: D  463 PHE cc_start: 0.6598 (t80) cc_final: 0.6388 (t80)
  outliers start: 22
  outliers final: 17
  residues processed: 76
  average time/residue: 0.0839
  time to fit residues: 9.1981
Evaluate side-chains
  71 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 53
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
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  534 GLN
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain D residue  192 LYS
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  408 PHE
Chi-restraints excluded: chain D residue  438 LEU
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  465 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 86 optimal weight:    7.9990
   chunk 29 optimal weight:    0.0870
   chunk 99 optimal weight:   10.0000
   chunk 85 optimal weight:    7.9990
   chunk 45 optimal weight:    0.7980
   chunk 69 optimal weight:    8.9990
   chunk 82 optimal weight:    6.9990
   chunk 97 optimal weight:    7.9990
   chunk 44 optimal weight:    1.9990
   chunk 48 optimal weight:    9.9990
   chunk 90 optimal weight:    6.9990
   overall best weight:    3.3764

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 652 ASN
** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 282 HIS
** 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 = 0.4190 r_free = 0.4190 target = 0.103692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.091670 restraints weight = 41038.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.092095 restraints weight = 34783.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.092356 restraints weight = 33058.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.092617 restraints weight = 25790.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.092768 restraints weight = 24258.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5835
moved from start:          0.6289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7784  Z= 0.200
  Angle     :  0.679   9.735  10637  Z= 0.366
  Chirality :  0.046   0.148   1290
  Planarity :  0.005   0.047   1422
  Dihedral  :  5.673  30.596   1195
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 13.33 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.14 (0.25), residues: 1138
  helix:  1.39 (0.24), residues: 425
  sheet: -0.34 (0.31), residues: 234
  loop : -0.81 (0.30), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 584 
 TYR   0.031   0.002   TYR D 486 
 PHE   0.024   0.003   PHE D 439 
 TRP   0.020   0.002   TRP D 245 
 HIS   0.007   0.002   HIS B 574 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 7784)
  covalent geometry    : angle       0.67939 (10637)
  hydrogen bonds       : bond        0.04742 (  465)
  hydrogen bonds       : angle       5.16474 ( 1341)

*********************** 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
  88 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 61
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  198 TRP cc_start: 0.6697 (m-90) cc_final: 0.6066 (m100)
REVERT: D  241 GLU cc_start: 0.5718 (tp30) cc_final: 0.5415 (tp30)
REVERT: D  256 TRP cc_start: 0.6427 (OUTLIER) cc_final: 0.6207 (m-10)
REVERT: D  386 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7793 (t80)
REVERT: D  439 PHE cc_start: 0.4293 (OUTLIER) cc_final: 0.3268 (p90)
REVERT: D  463 PHE cc_start: 0.6970 (t80) cc_final: 0.6711 (t80)
  outliers start: 27
  outliers final: 17
  residues processed: 81
  average time/residue: 0.0733
  time to fit residues: 8.9311
Evaluate side-chains
  73 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 53
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
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  534 GLN
Chi-restraints excluded: chain B residue  580 VAL
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  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  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  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 10 optimal weight:    0.9980
   chunk 94 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   chunk 103 optimal weight:   30.0000
   chunk 47 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 111 optimal weight:   30.0000
   chunk 109 optimal weight:   20.0000
   chunk 105 optimal weight:   20.0000
   overall best weight:    2.7186

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 652 ASN
** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4192 r_free = 0.4192 target = 0.103507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.091421 restraints weight = 41131.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.091622 restraints weight = 33683.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.092311 restraints weight = 28755.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.092497 restraints weight = 23603.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.092632 restraints weight = 23420.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5852
moved from start:          0.6709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7784  Z= 0.174
  Angle     :  0.657   8.734  10637  Z= 0.349
  Chirality :  0.045   0.137   1290
  Planarity :  0.004   0.044   1422
  Dihedral  :  5.467  28.517   1195
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 14.53 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.25), residues: 1138
  helix:  1.54 (0.25), residues: 428
  sheet: -0.53 (0.32), residues: 237
  loop : -0.96 (0.30), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 447 
 TYR   0.027   0.002   TYR D 486 
 PHE   0.030   0.003   PHE B 516 
 TRP   0.018   0.002   TRP D 245 
 HIS   0.010   0.002   HIS D 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 7784)
  covalent geometry    : angle       0.65716 (10637)
  hydrogen bonds       : bond        0.04488 (  465)
  hydrogen bonds       : angle       5.11459 ( 1341)

*********************** 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
  86 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 59
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: D  198 TRP cc_start: 0.6670 (m-90) cc_final: 0.6040 (m100)
REVERT: D  386 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7819 (t80)
REVERT: D  439 PHE cc_start: 0.4524 (OUTLIER) cc_final: 0.3313 (p90)
REVERT: D  463 PHE cc_start: 0.6934 (t80) cc_final: 0.6623 (t80)
  outliers start: 27
  outliers final: 20
  residues processed: 77
  average time/residue: 0.0783
  time to fit residues: 8.9840
Evaluate side-chains
  75 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 53
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
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  534 GLN
Chi-restraints excluded: chain B residue  588 GLN
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain B residue  649 ILE
Chi-restraints excluded: chain D residue  183 LEU
Chi-restraints excluded: chain D residue  205 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  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  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 80 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9980
   chunk 70 optimal weight:   10.0000
   chunk 23 optimal weight:    6.9990
   chunk 106 optimal weight:    8.9990
   chunk 84 optimal weight:   20.0000
   chunk 22 optimal weight:    1.9990
   chunk 89 optimal weight:   20.0000
   chunk 35 optimal weight:    0.0010
   chunk 53 optimal weight:    6.9990
   chunk 95 optimal weight:    3.9990
   overall best weight:    2.5992

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

Flipped N/Q/H residues before XYZ refinement:
B 605 ASN
** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4189 r_free = 0.4189 target = 0.103270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.091450 restraints weight = 40800.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.091963 restraints weight = 35073.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.092464 restraints weight = 30596.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.092685 restraints weight = 24293.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.092864 restraints weight = 22533.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5871
moved from start:          0.7010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7784  Z= 0.170
  Angle     :  0.643   8.592  10637  Z= 0.343
  Chirality :  0.045   0.175   1290
  Planarity :  0.004   0.042   1422
  Dihedral  :  5.401  28.273   1195
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 14.70 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.25), residues: 1138
  helix:  1.63 (0.25), residues: 428
  sheet: -0.63 (0.33), residues: 233
  loop : -1.04 (0.30), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 584 
 TYR   0.018   0.002   TYR D 486 
 PHE   0.022   0.002   PHE B 516 
 TRP   0.017   0.002   TRP D 245 
 HIS   0.008   0.002   HIS D 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 7784)
  covalent geometry    : angle       0.64329 (10637)
  hydrogen bonds       : bond        0.04383 (  465)
  hydrogen bonds       : angle       5.09427 ( 1341)

*********************** 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: 27
    poor density    : 58
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: B  447 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7307 (ttt180)
REVERT: B  535 PHE cc_start: 0.4652 (OUTLIER) cc_final: 0.3672 (t80)
REVERT: B  674 TYR cc_start: 0.2373 (OUTLIER) cc_final: 0.0471 (m-80)
REVERT: D  198 TRP cc_start: 0.6653 (m-90) cc_final: 0.5967 (m100)
REVERT: D  241 GLU cc_start: 0.5748 (tp30) cc_final: 0.5428 (tp30)
REVERT: D  386 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7842 (t80)
REVERT: D  439 PHE cc_start: 0.4491 (OUTLIER) cc_final: 0.3172 (p90)
  outliers start: 27
  outliers final: 20
  residues processed: 77
  average time/residue: 0.0775
  time to fit residues: 8.9328
Evaluate side-chains
  80 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 56
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
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  534 GLN
Chi-restraints excluded: chain B residue  535 PHE
Chi-restraints excluded: chain B residue  536 ASP
Chi-restraints excluded: chain B residue  588 GLN
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain B residue  649 ILE
Chi-restraints excluded: chain B residue  674 TYR
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 65 optimal weight:    6.9990
   chunk 99 optimal weight:   10.0000
   chunk 23 optimal weight:    7.9990
   chunk 32 optimal weight:    5.9990
   chunk 45 optimal weight:    7.9990
   chunk 98 optimal weight:   10.0000
   chunk 109 optimal weight:   30.0000
   chunk 26 optimal weight:    1.9990
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 588 GLN
B 622 HIS
** B 630 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 = 0.4171 r_free = 0.4171 target = 0.101850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.090041 restraints weight = 41353.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.090193 restraints weight = 36258.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.090797 restraints weight = 33416.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.091229 restraints weight = 25610.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.091398 restraints weight = 23880.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5976
moved from start:          0.7614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7784  Z= 0.214
  Angle     :  0.704   9.303  10637  Z= 0.380
  Chirality :  0.047   0.262   1290
  Planarity :  0.005   0.042   1422
  Dihedral  :  5.853  29.582   1195
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 16.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 15.04 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.30 (0.25), residues: 1138
  helix:  1.31 (0.25), residues: 420
  sheet: -0.84 (0.33), residues: 227
  loop : -1.18 (0.29), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 283 
 TYR   0.026   0.002   TYR D 437 
 PHE   0.024   0.003   PHE D 350 
 TRP   0.020   0.002   TRP D 245 
 HIS   0.009   0.002   HIS D 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 7784)
  covalent geometry    : angle       0.70425 (10637)
  hydrogen bonds       : bond        0.04879 (  465)
  hydrogen bonds       : angle       5.51421 ( 1341)

*********************** 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
  85 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 56
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: B  447 ARG cc_start: 0.7716 (mtt180) cc_final: 0.7197 (ttt180)
REVERT: B  535 PHE cc_start: 0.4582 (OUTLIER) cc_final: 0.3782 (t80)
REVERT: B  674 TYR cc_start: 0.2247 (OUTLIER) cc_final: 0.0317 (m-80)
REVERT: D  241 GLU cc_start: 0.5755 (tp30) cc_final: 0.5548 (tp30)
REVERT: D  271 GLN cc_start: 0.7763 (tp-100) cc_final: 0.7519 (tp-100)
REVERT: D  386 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7910 (t80)
REVERT: D  439 PHE cc_start: 0.4848 (OUTLIER) cc_final: 0.3393 (p90)
  outliers start: 29
  outliers final: 23
  residues processed: 76
  average time/residue: 0.0791
  time to fit residues: 9.0045
Evaluate side-chains
  80 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 53
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
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  534 GLN
Chi-restraints excluded: chain B residue  535 PHE
Chi-restraints excluded: chain B residue  536 ASP
Chi-restraints excluded: chain B residue  588 GLN
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain B residue  649 ILE
Chi-restraints excluded: chain B residue  674 TYR
Chi-restraints excluded: chain D residue  183 LEU
Chi-restraints excluded: chain D residue  205 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  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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 61 optimal weight:    0.0870
   chunk 31 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 49 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 7 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 95 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   chunk 5 optimal weight:    7.9990
   overall best weight:    1.3562

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

Flipped N/Q/H residues before XYZ refinement:
B 588 GLN
B 630 GLN
D 143 GLN
** D 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.104161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.092319 restraints weight = 40875.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.092214 restraints weight = 34021.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.092949 restraints weight = 30357.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.093197 restraints weight = 24105.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.093352 restraints weight = 22663.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5868
moved from start:          0.7540

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= 0.132
  Angle     :  0.623  13.044  10637  Z= 0.327
  Chirality :  0.044   0.189   1290
  Planarity :  0.004   0.041   1422
  Dihedral  :  5.253  27.532   1195
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 16.24 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.26), residues: 1138
  helix:  1.98 (0.25), residues: 421
  sheet: -0.88 (0.33), residues: 240
  loop : -0.99 (0.30), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 447 
 TYR   0.034   0.002   TYR D 437 
 PHE   0.024   0.002   PHE B 516 
 TRP   0.027   0.002   TRP D 188 
 HIS   0.011   0.001   HIS D 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 7784)
  covalent geometry    : angle       0.62325 (10637)
  hydrogen bonds       : bond        0.04123 (  465)
  hydrogen bonds       : angle       5.02715 ( 1341)

*********************** 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
  84 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 62
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: B  447 ARG cc_start: 0.7706 (mtt180) cc_final: 0.7189 (ttt180)
REVERT: B  535 PHE cc_start: 0.4522 (OUTLIER) cc_final: 0.3552 (t80)
REVERT: B  577 ASP cc_start: 0.6034 (m-30) cc_final: 0.5068 (p0)
REVERT: B  639 MET cc_start: 0.5706 (OUTLIER) cc_final: 0.5452 (tpp)
REVERT: B  674 TYR cc_start: 0.2465 (OUTLIER) cc_final: 0.0832 (m-80)
REVERT: D  165 THR cc_start: 0.6386 (p) cc_final: 0.6126 (p)
REVERT: D  198 TRP cc_start: 0.6646 (m-90) cc_final: 0.5828 (m100)
REVERT: D  386 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7804 (t80)
REVERT: D  439 PHE cc_start: 0.4464 (OUTLIER) cc_final: 0.2919 (p90)
REVERT: D  463 PHE cc_start: 0.6808 (t80) cc_final: 0.6555 (t80)
  outliers start: 22
  outliers final: 15
  residues processed: 78
  average time/residue: 0.0757
  time to fit residues: 8.7255
Evaluate side-chains
  76 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 56
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
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  535 PHE
Chi-restraints excluded: chain B residue  536 ASP
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain B residue  649 ILE
Chi-restraints excluded: chain B residue  674 TYR
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  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  451 PHE
Chi-restraints excluded: chain D residue  486 TYR
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 67 optimal weight:    4.9990
   chunk 97 optimal weight:   20.0000
   chunk 95 optimal weight:    6.9990
   chunk 69 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 74 optimal weight:    0.0170
   chunk 59 optimal weight:    8.9990
   chunk 53 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 79 optimal weight:   20.0000
   chunk 25 optimal weight:    6.9990
   overall best weight:    2.2026

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

Flipped N/Q/H residues before XYZ refinement:
** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 534 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 = 0.4201 r_free = 0.4201 target = 0.103373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.091552 restraints weight = 40525.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.091998 restraints weight = 32783.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.092361 restraints weight = 31102.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.092638 restraints weight = 23901.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.092872 restraints weight = 22039.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5891
moved from start:          0.7752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7784  Z= 0.155
  Angle     :  0.648  12.695  10637  Z= 0.341
  Chirality :  0.045   0.155   1290
  Planarity :  0.004   0.040   1422
  Dihedral  :  5.275  28.006   1195
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 16.92 %
    Favored  : 79.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.26), residues: 1138
  helix:  1.97 (0.25), residues: 426
  sheet: -0.86 (0.33), residues: 237
  loop : -1.04 (0.30), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 447 
 TYR   0.026   0.002   TYR D 437 
 PHE   0.021   0.002   PHE B 516 
 TRP   0.018   0.002   TRP D 188 
 HIS   0.010   0.002   HIS D 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 7784)
  covalent geometry    : angle       0.64767 (10637)
  hydrogen bonds       : bond        0.04255 (  465)
  hydrogen bonds       : angle       5.09206 ( 1341)

********************** 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
  80 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 57
  time to evaluate  : 0.394 
Fit side-chains
REVERT: B  447 ARG cc_start: 0.7676 (mtt180) cc_final: 0.7196 (ttt180)
REVERT: B  534 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.6519 (tt0)
REVERT: B  535 PHE cc_start: 0.4283 (OUTLIER) cc_final: 0.3491 (t80)
REVERT: B  577 ASP cc_start: 0.6012 (m-30) cc_final: 0.5229 (p0)
REVERT: B  674 TYR cc_start: 0.2607 (OUTLIER) cc_final: 0.0925 (m-80)
REVERT: D  165 THR cc_start: 0.6668 (p) cc_final: 0.6353 (p)
REVERT: D  198 TRP cc_start: 0.6618 (m-90) cc_final: 0.5881 (m100)
REVERT: D  241 GLU cc_start: 0.5616 (tp30) cc_final: 0.5343 (tp30)
REVERT: D  386 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7891 (t80)
REVERT: D  439 PHE cc_start: 0.4655 (OUTLIER) cc_final: 0.3289 (p90)
REVERT: D  463 PHE cc_start: 0.7071 (t80) cc_final: 0.6652 (t80)
  outliers start: 23
  outliers final: 18
  residues processed: 75
  average time/residue: 0.0830
  time to fit residues: 9.0912
Evaluate side-chains
  77 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 54
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
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  534 GLN
Chi-restraints excluded: chain B residue  535 PHE
Chi-restraints excluded: chain B residue  536 ASP
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  639 MET
Chi-restraints excluded: chain B residue  649 ILE
Chi-restraints excluded: chain B residue  674 TYR
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  301 ILE
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  451 PHE
Chi-restraints excluded: chain D residue  486 TYR
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
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 65.9012 > 50:
  distance: 40 - 138:  14.767
  distance: 43 - 135:  15.262
  distance: 56 - 123:  22.251
  distance: 59 - 120:  20.150
  distance: 84 - 88:  29.558
  distance: 88 - 89:  17.726
  distance: 89 - 90:  33.471
  distance: 89 - 92:  27.455
  distance: 90 - 91:   8.148
  distance: 92 - 93:  28.737
  distance: 93 - 94:  14.984
  distance: 94 - 95:  25.458
  distance: 94 - 96:  30.838
  distance: 97 - 98:  34.578
  distance: 98 - 99:  31.272
  distance: 98 - 101:  34.144
  distance: 99 - 100:  24.933
  distance: 99 - 106:  22.707
  distance: 101 - 102:  24.795
  distance: 102 - 103:  16.869
  distance: 103 - 104:  41.660
  distance: 104 - 105:  31.623
  distance: 106 - 107:  20.930
  distance: 106 - 112:  21.789
  distance: 107 - 108:  37.928
  distance: 107 - 110:  39.108
  distance: 108 - 109:   3.444
  distance: 108 - 113:  23.620
  distance: 110 - 111:  40.643
  distance: 111 - 112:  12.056
  distance: 113 - 114:  13.870
  distance: 114 - 115:  13.698
  distance: 114 - 117:  31.158
  distance: 115 - 116:  26.346
  distance: 115 - 120:  22.320
  distance: 117 - 118:   5.416
  distance: 117 - 119:   6.845
  distance: 120 - 121:  20.712
  distance: 121 - 122:  10.682
  distance: 121 - 124:  30.132
  distance: 122 - 123:  13.064
  distance: 122 - 127:  16.904
  distance: 124 - 125:  18.336
  distance: 124 - 126:  38.311
  distance: 127 - 128:  28.240
  distance: 128 - 129:  40.679
  distance: 128 - 131:  59.006
  distance: 129 - 130:  17.751
  distance: 129 - 135:  36.961
  distance: 131 - 132:  65.901
  distance: 132 - 133:  48.400
  distance: 132 - 134:  56.393
  distance: 135 - 136:  14.954
  distance: 136 - 137:   8.019
  distance: 136 - 139:  20.487
  distance: 137 - 138:  15.134
  distance: 137 - 143:  10.177
  distance: 139 - 140:  26.134
  distance: 139 - 141:  10.951
  distance: 140 - 142:  18.633
  distance: 143 - 144:   5.897
  distance: 144 - 145:   9.283
  distance: 144 - 147:  10.802
  distance: 145 - 146:  18.314
  distance: 145 - 152:  23.452
  distance: 147 - 148:  12.817
  distance: 148 - 149:  22.540
  distance: 149 - 150:  24.947
  distance: 150 - 151:  19.872
  distance: 152 - 153:  16.363
  distance: 153 - 154:  29.682
  distance: 153 - 156:  32.128
  distance: 154 - 155:  33.964
  distance: 154 - 161:  37.675
  distance: 156 - 157:  40.992
  distance: 157 - 158:  10.880
  distance: 158 - 159:  22.692
  distance: 158 - 160:  25.720
  distance: 161 - 162:  43.622
  distance: 162 - 163:  26.720
  distance: 162 - 165:  37.663
  distance: 163 - 164:  17.098
  distance: 163 - 168:  20.317
  distance: 165 - 166:  40.572
  distance: 165 - 167:  39.607