Starting phenix.real_space_refine
on Wed Mar 12 08:55:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x2l_38016/03_2025/8x2l_38016.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x2l_38016/03_2025/8x2l_38016.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x2l_38016/03_2025/8x2l_38016.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x2l_38016/03_2025/8x2l_38016.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x2l_38016/03_2025/8x2l_38016.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x2l_38016/03_2025/8x2l_38016.cif"
  }
  resolution = 2.99
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.011 sd=   0.067
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: 7
    Type Number    sf(0)   Gaussians
     Fe      2      7.16       5
     P       2      5.49       5
     Mg      1      5.21       5
     S      34      5.16       5
     C    4639      2.51       5
     N    1168      2.21       5
     O    1253      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7099
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1030
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 134, 1030
          Classifications: {'peptide': 134}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 128}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 4108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 525, 4108
          Classifications: {'peptide': 525}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 502}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 140
          Unresolved non-hydrogen angles: 172
          Unresolved non-hydrogen dihedrals: 110
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 105
    Chain: "H"
      Number of atoms: 935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 935
          Classifications: {'peptide': 119}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 5, 'TRANS': 113}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "L"
      Number of atoms: 818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 818
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 13
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "B"
      Number of atoms: 169
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 169
          Unusual residues: {' MG': 1, 'FAD': 1, 'HEM': 2, 'NAG': 2}
          Classifications: {'undetermined': 6, 'water': 1}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 5.24, per 1000 atoms: 0.74
  Number of scatterers: 7099
  At special positions: 0
  Unit cell: (72.988, 84.296, 152.144, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Fe      2     26.01
     S      34     16.00
     P       2     15.00
     Mg      1     11.99
     O    1253      8.00
     N    1168      7.00
     C    4639      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 244 " - pdb=" SG  CYS B 257 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04

  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=3, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
    NAG-ASN
      " NAG B 604 " - " ASN B 132 "
      " NAG B 605 " - " ASN B 240 "
      " NAG C   1 " - " ASN B 149 "
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.17
  Conformation dependent library (CDL) restraints added in 832.5 milliseconds
  

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1644

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 10 sheets defined
      48.0% alpha, 16.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 31
      removed outlier: 4.377A  pdb=" N   TRP A   9 " --> pdb=" O   GLU A   5 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ALA A  16 " --> pdb=" O   GLU A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 54
    Processing helix  chain 'A' and resid 69 through 80
      removed outlier: 4.557A  pdb=" N   MET A  73 " --> pdb=" O   GLY A  69 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   PHE A  80 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 84
    Processing helix  chain 'A' and resid 86 through 99
    Processing helix  chain 'A' and resid 100 through 103
      removed outlier: 3.987A  pdb=" N   PHE A 103 " --> pdb=" O   PRO A 100 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 100 through 103'
    Processing helix  chain 'A' and resid 104 through 128
      removed outlier: 4.353A  pdb=" N   LEU A 109 " --> pdb=" O   LEU A 105 " (cutoff:3.500A)
      removed outlier: 5.403A  pdb=" N   GLY A 110 " --> pdb=" O   ALA A 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 9 through 32
      removed outlier: 3.718A  pdb=" N   LEU B  25 " --> pdb=" O   LEU B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 40
    Processing helix  chain 'B' and resid 41 through 46
    Processing helix  chain 'B' and resid 47 through 49
      No H-bonds generated for 'chain 'B' and resid 47 through 49'
    Processing helix  chain 'B' and resid 50 through 69
      Proline residue:  B  56  - end of helix
      removed outlier: 3.595A  pdb=" N   MET B  65 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   LEU B  68 " --> pdb=" O   CYS B  64 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU B  69 " --> pdb=" O   MET B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 83
    Processing helix  chain 'B' and resid 89 through 95
    Processing helix  chain 'B' and resid 96 through 129
      removed outlier: 3.518A  pdb=" N   ALA B 129 " --> pdb=" O   TRP B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 143
    Processing helix  chain 'B' and resid 163 through 173
    Processing helix  chain 'B' and resid 173 through 192
    Processing helix  chain 'B' and resid 194 through 201
    Processing helix  chain 'B' and resid 201 through 209
    Processing helix  chain 'B' and resid 211 through 221
    Processing helix  chain 'B' and resid 232 through 239
    Processing helix  chain 'B' and resid 240 through 245
    Processing helix  chain 'B' and resid 247 through 251
    Processing helix  chain 'B' and resid 268 through 293
      removed outlier: 3.503A  pdb=" N   TRP B 272 " --> pdb=" O   MET B 268 " (cutoff:3.500A)
      removed outlier: 5.206A  pdb=" N   GLY B 275 " --> pdb=" O   LYS B 271 " (cutoff:3.500A)
      Proline residue:  B 276  - end of helix
    Processing helix  chain 'B' and resid 359 through 370
    Processing helix  chain 'B' and resid 397 through 401
      removed outlier: 3.699A  pdb=" N   TYR B 401 " --> pdb=" O   VAL B 398 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 430
      removed outlier: 3.768A  pdb=" N   SER B 418 " --> pdb=" O   THR B 414 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ASN B 430 " --> pdb=" O   LYS B 426 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 468
    Processing helix  chain 'B' and resid 515 through 527
    Processing helix  chain 'B' and resid 539 through 554
    Processing helix  chain 'H' and resid 62 through 65
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.590A  pdb=" N   THR H  91 " --> pdb=" O   THR H  88 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.811A  pdb=" N   ILE L  83 " --> pdb=" O   GLN L  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 229 through 231
    Processing sheet with id=AA2, first strand: chain 'B' and resid 295 through 303
      removed outlier: 7.109A  pdb=" N   GLN B 311 " --> pdb=" O   THR B 298 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   VAL B 300 " --> pdb=" O   GLU B 309 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   GLU B 309 " --> pdb=" O   VAL B 300 " (cutoff:3.500A)
      removed outlier: 4.918A  pdb=" N   THR B 302 " --> pdb=" O   THR B 307 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   THR B 307 " --> pdb=" O   THR B 302 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 338 through 341
      removed outlier: 4.345A  pdb=" N   PHE B 326 " --> pdb=" O   GLY B 389 " (cutoff:3.500A)
      removed outlier: 5.470A  pdb=" N   GLY B 389 " --> pdb=" O   PHE B 326 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   LYS B 328 " --> pdb=" O   VAL B 387 " (cutoff:3.500A)
      removed outlier: 5.365A  pdb=" N   VAL B 387 " --> pdb=" O   LYS B 328 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 509 through 511
      removed outlier: 8.295A  pdb=" N   LEU B 510 " --> pdb=" O   TYR B 476 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   ILE B 478 " --> pdb=" O   LEU B 510 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   ILE B 439 " --> pdb=" O   SER B 475 " (cutoff:3.500A)
      removed outlier: 7.868A  pdb=" N   ASN B 477 " --> pdb=" O   ILE B 439 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   PHE B 441 " --> pdb=" O   ASN B 477 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   TYR B 479 " --> pdb=" O   PHE B 441 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   TRP B 443 " --> pdb=" O   TYR B 479 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   VAL B 404 " --> pdb=" O   LYS B 438 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL B 403 " --> pdb=" O   ARG B 531 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA B 409 " --> pdb=" O   CYS B 537 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   ILE B 532 " --> pdb=" O   ILE B 564 " (cutoff:3.500A)
      removed outlier: 7.291A  pdb=" N   ASN B 566 " --> pdb=" O   ILE B 532 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   VAL B 534 " --> pdb=" O   ASN B 566 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 4 through 7
    Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.678A  pdb=" N   LYS H  45 " --> pdb=" O   PHE H  41 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60
      removed outlier: 3.833A  pdb=" N   PHE H 108 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6
      removed outlier: 3.524A  pdb=" N   ASP L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13
    Processing sheet with id=AB1, first strand: chain 'L' and resid 53 through 54
      removed outlier: 6.572A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 4.983A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)

    358 hydrogen bonds defined for protein.
    1011 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.04

  Time building geometry restraints manager: 2.50 seconds

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

  Histogram of bond lengths:
        1.22 -     1.39: 2962
        1.39 -     1.56: 4282
        1.56 -     1.74: 4
        1.74 -     1.91: 48
        1.91 -     2.08: 8
  Bond restraints: 7304
  Sorted by residual:
  bond pdb=" C5X FAD B 601 "
       pdb=" C9A FAD B 601 "
    ideal  model  delta    sigma   weight residual
    1.412  1.499 -0.087 2.00e-02 2.50e+03 1.88e+01
  bond pdb=" C4A FAD B 601 "
       pdb=" C5A FAD B 601 "
    ideal  model  delta    sigma   weight residual
    1.386  1.471 -0.085 2.00e-02 2.50e+03 1.81e+01
  bond pdb=" C5A FAD B 601 "
       pdb=" C6A FAD B 601 "
    ideal  model  delta    sigma   weight residual
    1.407  1.479 -0.072 2.00e-02 2.50e+03 1.31e+01
  bond pdb=" C7  FAD B 601 "
       pdb=" C8  FAD B 601 "
    ideal  model  delta    sigma   weight residual
    1.420  1.491 -0.071 2.00e-02 2.50e+03 1.25e+01
  bond pdb=" C4X FAD B 601 "
       pdb=" N5  FAD B 601 "
    ideal  model  delta    sigma   weight residual
    1.288  1.349 -0.061 2.00e-02 2.50e+03 9.45e+00
  ... (remaining 7299 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 9622
        1.89 -     3.78: 288
        3.78 -     5.67: 61
        5.67 -     7.56: 6
        7.56 -     9.45: 2
  Bond angle restraints: 9979
  Sorted by residual:
  angle pdb=" P   FAD B 601 "
        pdb=" O3P FAD B 601 "
        pdb=" PA  FAD B 601 "
      ideal   model   delta    sigma   weight residual
     130.34  120.89    9.45 3.00e+00 1.11e-01 9.93e+00
  angle pdb=" C2A FAD B 601 "
        pdb=" N3A FAD B 601 "
        pdb=" C4A FAD B 601 "
      ideal   model   delta    sigma   weight residual
     111.66  120.72   -9.06 3.00e+00 1.11e-01 9.12e+00
  angle pdb=" C   MET B  65 "
        pdb=" N   LEU B  66 "
        pdb=" CA  LEU B  66 "
      ideal   model   delta    sigma   weight residual
     121.18  116.07    5.11 1.98e+00 2.55e-01 6.67e+00
  angle pdb=" C5A FAD B 601 "
        pdb=" C4A FAD B 601 "
        pdb=" N3A FAD B 601 "
      ideal   model   delta    sigma   weight residual
     126.50  119.07    7.43 3.00e+00 1.11e-01 6.14e+00
  angle pdb=" C   ASN B 430 "
        pdb=" N   ALA B 431 "
        pdb=" CA  ALA B 431 "
      ideal   model   delta    sigma   weight residual
     121.54  126.02   -4.48 1.91e+00 2.74e-01 5.51e+00
  ... (remaining 9974 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.31: 4163
       31.31 -    62.61: 72
       62.61 -    93.92: 15
       93.92 -   125.23: 4
      125.23 -   156.53: 1
  Dihedral angle restraints: 4255
    sinusoidal: 1694
      harmonic: 2561
  Sorted by residual:
  dihedral pdb=" O5' FAD B 601 "
           pdb=" O3P FAD B 601 "
           pdb=" P   FAD B 601 "
           pdb=" PA  FAD B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     298.23  141.70  156.53     1      3.00e+01 1.11e-03 2.05e+01
  dihedral pdb=" CA  LEU B 335 "
           pdb=" C   LEU B 335 "
           pdb=" N   GLU B 336 "
           pdb=" CA  GLU B 336 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.93  -22.07     0      5.00e+00 4.00e-02 1.95e+01
  dihedral pdb=" CA  ASP B 388 "
           pdb=" C   ASP B 388 "
           pdb=" N   GLY B 389 "
           pdb=" CA  GLY B 389 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.17   20.83     0      5.00e+00 4.00e-02 1.73e+01
  ... (remaining 4252 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 904
       0.054 -    0.107: 171
       0.107 -    0.161: 41
       0.161 -    0.214: 0
       0.214 -    0.268: 2
  Chirality restraints: 1118
  Sorted by residual:
  chirality pdb=" C1  BMA C   3 "
            pdb=" O4  NAG C   2 "
            pdb=" C2  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.34   -0.06 2.00e-02 2.50e+03 9.23e+00
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.46    0.06 2.00e-02 2.50e+03 7.96e+00
  chirality pdb=" C3B FAD B 601 "
            pdb=" C2B FAD B 601 "
            pdb=" C4B FAD B 601 "
            pdb=" O3B FAD B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.72   -2.45   -0.27 2.00e-01 2.50e+01 1.80e+00
  ... (remaining 1115 not shown)

  Planarity restraints: 1212
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B  20 "    0.015 2.00e-02 2.50e+03   3.05e-02 9.31e+00
        pdb=" C   GLY B  20 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   GLY B  20 "    0.020 2.00e-02 2.50e+03
        pdb=" N   LEU B  21 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B  36 "   -0.043 5.00e-02 4.00e+02   6.49e-02 6.74e+00
        pdb=" N   PRO B  37 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO B  37 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B  37 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 329 "    0.038 5.00e-02 4.00e+02   5.84e-02 5.45e+00
        pdb=" N   PRO B 330 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO B 330 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 330 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1209 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 101
        2.66 -     3.22: 6889
        3.22 -     3.78: 11723
        3.78 -     4.34: 16434
        4.34 -     4.90: 26350
  Nonbonded interactions: 61497
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS B 222 "
            pdb="FE   HEM B 602 "
     model   vdw
     2.102 3.080
  nonbonded pdb=" OE1 GLU A  53 "
            pdb=" OH  TYR A 121 "
     model   vdw
     2.106 3.040
  nonbonded pdb=" CE1 HIS B 209 "
            pdb="FE   HEM B 603 "
     model   vdw
     2.194 2.576
  nonbonded pdb=" O   TYR L  50 "
            pdb=" OG1 THR L  51 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OH  TYR B 207 "
            pdb=" OE2 GLU B 336 "
     model   vdw
     2.228 3.040
  ... (remaining 61492 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     20.750
  Find NCS groups from input model:        0.070
  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:             0.010
  Load rotamer database and sin/cos tables:14.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
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      :  0.006   0.087   7304  Z= 0.380
  Angle     :  0.798   9.455   9979  Z= 0.385
  Chirality :  0.046   0.268   1118
  Planarity :  0.006   0.065   1209
  Dihedral  : 13.826 156.533   2602
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  1.12 %
    Favored  : 98.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.28), residues: 871
  helix:  0.31 (0.26), residues: 367
  sheet: -0.56 (0.34), residues: 199
  loop : -0.35 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  18 
 HIS   0.010   0.002   HIS B 209 
 PHE   0.020   0.002   PHE B  62 
 TYR   0.014   0.002   TYR B 201 
 ARG   0.005   0.001   ARG B  43 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 180
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  416 PHE cc_start: 0.7890 (m-80) cc_final: 0.7604 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 181
  average time/residue: 1.0996
  time to fit residues: 210.8866
Evaluate side-chains
  115 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.6980
   chunk 65 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 43 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 67 optimal weight:    0.6980
   chunk 26 optimal weight:    0.3980
   chunk 40 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  70 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 ASN
B 210 HIS
B 265 ASN
B 293 GLN
B 527 HIS
B 566 ASN
H   5 GLN
L   6 GLN
L  90 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.124824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.108723 restraints weight = 11021.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 1.37
r_work: 0.3498 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3382 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.2173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7304  Z= 0.289
  Angle     :  0.669  11.829   9979  Z= 0.321
  Chirality :  0.045   0.196   1118
  Planarity :  0.005   0.056   1209
  Dihedral  :  9.896 156.924   1118
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 12.32 %
    Favored  : 83.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.28), residues: 871
  helix:  0.91 (0.27), residues: 360
  sheet: -0.52 (0.35), residues: 202
  loop : -0.18 (0.37), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 424 
 HIS   0.006   0.002   HIS B 111 
 PHE   0.027   0.002   PHE B  62 
 TYR   0.018   0.002   TYR A  88 
 ARG   0.005   0.001   ARG B 159 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 139
  time to evaluate  : 0.728 
Fit side-chains
   revert: symmetry clash
REVERT: B  349 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7414 (m-30)
REVERT: B  402 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6358 (tp30)
REVERT: H   84 ASN cc_start: 0.7949 (OUTLIER) cc_final: 0.7429 (m-40)
REVERT: L   89 GLN cc_start: 0.8526 (tt0) cc_final: 0.8261 (tt0)
  outliers start: 30
  outliers final: 11
  residues processed: 154
  average time/residue: 0.9929
  time to fit residues: 163.6553
Evaluate side-chains
  136 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue   71 LYS
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain B residue   67 ILE
Chi-restraints excluded: chain B residue  242 THR
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  349 ASP
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain H residue   84 ASN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   58 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 46 optimal weight:    6.9990
   chunk 72 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 63 optimal weight:    7.9990
   chunk 0 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 70 optimal weight:    0.7980
   chunk 76 optimal weight:    0.0270
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
A  70 GLN
A 130 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 ASN
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 527 HIS
H  40 GLN
L  38 GLN
L  55 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.122367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.106026 restraints weight = 11124.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 1.38
r_work: 0.3453 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3345 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.2785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7304  Z= 0.272
  Angle     :  0.635  11.563   9979  Z= 0.299
  Chirality :  0.043   0.199   1118
  Planarity :  0.005   0.055   1209
  Dihedral  :  8.775 158.144   1118
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 15.13 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.28), residues: 871
  helix:  1.01 (0.26), residues: 366
  sheet: -0.39 (0.35), residues: 202
  loop : -0.13 (0.38), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 424 
 HIS   0.005   0.001   HIS B 115 
 PHE   0.021   0.002   PHE B 454 
 TYR   0.015   0.002   TYR B  29 
 ARG   0.005   0.001   ARG B 199 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 127
  time to evaluate  : 0.707 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.7551 (mp) cc_final: 0.7259 (mt)
REVERT: B  302 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.8108 (t)
REVERT: B  402 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6296 (tp30)
REVERT: H   84 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7489 (m-40)
  outliers start: 32
  outliers final: 14
  residues processed: 144
  average time/residue: 0.8500
  time to fit residues: 131.6400
Evaluate side-chains
  125 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LYS
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain B residue   67 ILE
Chi-restraints excluded: chain B residue  242 THR
Chi-restraints excluded: chain B residue  250 GLU
Chi-restraints excluded: chain B residue  302 THR
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  336 GLU
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain B residue  508 LYS
Chi-restraints excluded: chain B residue  509 THR
Chi-restraints excluded: chain H residue   84 ASN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   58 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0870
   chunk 40 optimal weight:    0.8980
   chunk 85 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0060
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.4174

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

Flipped N/Q/H residues before XYZ refinement:
A  70 GLN
A 130 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 111 HIS
** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 GLN
B 527 HIS
L  55 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.123223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.106335 restraints weight = 11266.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 1.49
r_work: 0.3468 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3348 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.3076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7304  Z= 0.221
  Angle     :  0.610  10.057   9979  Z= 0.284
  Chirality :  0.042   0.164   1118
  Planarity :  0.004   0.048   1209
  Dihedral  :  8.279 159.204   1118
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 15.83 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.28), residues: 871
  helix:  1.14 (0.26), residues: 371
  sheet: -0.23 (0.36), residues: 197
  loop : -0.33 (0.37), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 424 
 HIS   0.004   0.001   HIS B 115 
 PHE   0.018   0.001   PHE B 454 
 TYR   0.014   0.001   TYR B  29 
 ARG   0.004   0.001   ARG H  98 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 118
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.7755 (mp) cc_final: 0.7452 (mt)
REVERT: B  102 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.6676 (tttm)
REVERT: B  356 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7023 (mtt180)
REVERT: B  402 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.6034 (tp30)
REVERT: B  465 MET cc_start: 0.6914 (mmt) cc_final: 0.6606 (mmm)
REVERT: H   84 ASN cc_start: 0.8030 (OUTLIER) cc_final: 0.7483 (m-40)
  outliers start: 38
  outliers final: 14
  residues processed: 143
  average time/residue: 0.8922
  time to fit residues: 137.0469
Evaluate side-chains
  122 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LYS
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain B residue  102 LYS
Chi-restraints excluded: chain B residue  242 THR
Chi-restraints excluded: chain B residue  250 GLU
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  356 ARG
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain B residue  508 LYS
Chi-restraints excluded: chain B residue  546 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   84 ASN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   58 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 33 optimal weight:    0.3980
   chunk 27 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 38 optimal weight:    0.2980
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A  70 GLN
A 130 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 ASN
** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 265 ASN
** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 527 HIS
L  55 HIS
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.121705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.105301 restraints weight = 11015.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 1.36
r_work: 0.3448 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.3349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7304  Z= 0.252
  Angle     :  0.618  10.919   9979  Z= 0.289
  Chirality :  0.043   0.206   1118
  Planarity :  0.005   0.053   1209
  Dihedral  :  8.382 163.871   1118
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 17.51 %
    Favored  : 78.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.29), residues: 871
  helix:  1.18 (0.26), residues: 372
  sheet: -0.24 (0.36), residues: 199
  loop : -0.29 (0.38), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 106 
 HIS   0.006   0.001   HIS B 115 
 PHE   0.022   0.002   PHE B  13 
 TYR   0.022   0.002   TYR A  88 
 ARG   0.008   0.001   ARG B 531 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 117
  time to evaluate  : 0.830 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.7843 (mp) cc_final: 0.7542 (mt)
REVERT: B  102 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.6739 (tttm)
REVERT: B  356 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7061 (mtt180)
REVERT: B  402 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6100 (tp30)
REVERT: B  465 MET cc_start: 0.7003 (mmt) cc_final: 0.6645 (mmm)
REVERT: H   84 ASN cc_start: 0.8038 (OUTLIER) cc_final: 0.7468 (m-40)
REVERT: H  111 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.6449 (pm20)
  outliers start: 31
  outliers final: 13
  residues processed: 135
  average time/residue: 0.9380
  time to fit residues: 135.7417
Evaluate side-chains
  127 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LYS
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain B residue  102 LYS
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  356 ARG
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain B residue  508 LYS
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   84 ASN
Chi-restraints excluded: chain H residue  111 GLN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   77 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 81 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0060
   chunk 4 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   chunk 34 optimal weight:    0.4980
   chunk 23 optimal weight:    0.5980
   chunk 84 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
A  70 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 ASN
** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 265 ASN
B 527 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.119771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.102288 restraints weight = 11266.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 1.47
r_work: 0.3370 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.3521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7304  Z= 0.251
  Angle     :  0.622  10.755   9979  Z= 0.289
  Chirality :  0.042   0.195   1118
  Planarity :  0.004   0.047   1209
  Dihedral  :  8.432 164.978   1118
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 18.77 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.29), residues: 871
  helix:  1.36 (0.27), residues: 366
  sheet: -0.22 (0.36), residues: 199
  loop : -0.26 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 106 
 HIS   0.006   0.001   HIS B 115 
 PHE   0.017   0.001   PHE B 454 
 TYR   0.026   0.002   TYR B 201 
 ARG   0.005   0.001   ARG B 531 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 115
  time to evaluate  : 0.898 
Fit side-chains
REVERT: B  356 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7011 (mtt180)
REVERT: B  393 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7858 (p)
REVERT: B  402 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6041 (tp30)
REVERT: B  465 MET cc_start: 0.7048 (mmt) cc_final: 0.6736 (mmm)
REVERT: H   84 ASN cc_start: 0.8055 (OUTLIER) cc_final: 0.7532 (m-40)
REVERT: H  111 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.6416 (pm20)
  outliers start: 31
  outliers final: 12
  residues processed: 132
  average time/residue: 0.9710
  time to fit residues: 138.2635
Evaluate side-chains
  125 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LYS
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain B residue   65 MET
Chi-restraints excluded: chain B residue  250 GLU
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  356 ARG
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   84 ASN
Chi-restraints excluded: chain H residue  111 GLN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   77 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 54 optimal weight:    0.0370
   chunk 35 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   chunk 49 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 73 optimal weight:    0.1980
   chunk 67 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0050
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.3072

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 265 ASN
B 527 HIS
L  55 HIS
** L  89 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 = 0.3747 r_free = 0.3747 target = 0.121160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.103829 restraints weight = 11021.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 1.45
r_work: 0.3402 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.3661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7304  Z= 0.195
  Angle     :  0.592   9.062   9979  Z= 0.277
  Chirality :  0.041   0.159   1118
  Planarity :  0.004   0.046   1209
  Dihedral  :  8.332 162.895   1118
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 20.45 %
    Favored  : 75.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.29), residues: 871
  helix:  1.33 (0.26), residues: 372
  sheet: -0.22 (0.37), residues: 200
  loop : -0.32 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 289 
 HIS   0.005   0.001   HIS B 115 
 PHE   0.015   0.001   PHE B 416 
 TYR   0.026   0.001   TYR B 201 
 ARG   0.004   0.000   ARG B 531 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 0.766 
Fit side-chains
REVERT: B  246 GLN cc_start: 0.7730 (mp10) cc_final: 0.7498 (pm20)
REVERT: B  356 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7047 (mtt180)
REVERT: B  402 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.5993 (tp30)
REVERT: B  465 MET cc_start: 0.7026 (mmt) cc_final: 0.6721 (mmm)
REVERT: H   49 MET cc_start: 0.8507 (mtp) cc_final: 0.7887 (ptm)
REVERT: H   84 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7475 (m-40)
REVERT: H  111 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6424 (pm20)
  outliers start: 26
  outliers final: 13
  residues processed: 126
  average time/residue: 0.8754
  time to fit residues: 118.6886
Evaluate side-chains
  124 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 LYS
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  356 ARG
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain B residue  508 LYS
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   47 GLU
Chi-restraints excluded: chain H residue   84 ASN
Chi-restraints excluded: chain H residue  111 GLN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   77 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 13 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0470
   chunk 41 optimal weight:    0.0770
   chunk 67 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.4436

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 ASN
B 265 ASN
B 459 GLN
B 527 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.120574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.103243 restraints weight = 11070.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 1.45
r_work: 0.3389 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.3748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7304  Z= 0.228
  Angle     :  0.607   9.797   9979  Z= 0.284
  Chirality :  0.042   0.193   1118
  Planarity :  0.004   0.069   1209
  Dihedral  :  8.336 162.545   1118
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 19.47 %
    Favored  : 76.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.29), residues: 871
  helix:  1.37 (0.26), residues: 372
  sheet: -0.23 (0.37), residues: 200
  loop : -0.28 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP B 337 
 HIS   0.006   0.001   HIS B 115 
 PHE   0.017   0.001   PHE B 416 
 TYR   0.026   0.001   TYR B 201 
 ARG   0.005   0.000   ARG H  98 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 113
  time to evaluate  : 0.772 
Fit side-chains
REVERT: A   88 TYR cc_start: 0.7699 (m-10) cc_final: 0.7494 (m-10)
REVERT: B  246 GLN cc_start: 0.7722 (mp10) cc_final: 0.7509 (pm20)
REVERT: B  356 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7091 (mtt180)
REVERT: B  363 GLU cc_start: 0.7375 (tm-30) cc_final: 0.7061 (tt0)
REVERT: B  402 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.5840 (tp30)
REVERT: B  465 MET cc_start: 0.7072 (mmt) cc_final: 0.6745 (mmm)
REVERT: H   49 MET cc_start: 0.8509 (mtp) cc_final: 0.8120 (ptp)
REVERT: H   84 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7501 (m-40)
REVERT: H  111 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.6423 (pm20)
  outliers start: 27
  outliers final: 14
  residues processed: 126
  average time/residue: 0.9897
  time to fit residues: 135.0678
Evaluate side-chains
  128 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain B residue   65 MET
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  336 GLU
Chi-restraints excluded: chain B residue  356 ARG
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   47 GLU
Chi-restraints excluded: chain H residue   84 ASN
Chi-restraints excluded: chain H residue  111 GLN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   77 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0050
   chunk 17 optimal weight:    0.4980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 ASN
B 265 ASN
B 459 GLN
B 527 HIS
L  55 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.119275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.101792 restraints weight = 11228.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 1.45
r_work: 0.3369 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.3877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7304  Z= 0.265
  Angle     :  0.631  11.006   9979  Z= 0.293
  Chirality :  0.043   0.198   1118
  Planarity :  0.004   0.043   1209
  Dihedral  :  8.435 163.617   1118
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 20.31 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.29), residues: 871
  helix:  1.41 (0.27), residues: 366
  sheet: -0.30 (0.37), residues: 200
  loop : -0.28 (0.38), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 337 
 HIS   0.007   0.001   HIS B 115 
 PHE   0.016   0.002   PHE B 416 
 TYR   0.025   0.002   TYR B 201 
 ARG   0.005   0.001   ARG H  98 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.698 
Fit side-chains
REVERT: B  356 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7116 (mtt180)
REVERT: B  402 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.5803 (tp30)
REVERT: B  461 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7907 (mp)
REVERT: B  465 MET cc_start: 0.7109 (mmt) cc_final: 0.6755 (mmm)
REVERT: H   84 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7546 (m-40)
REVERT: H  111 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.6505 (pm20)
  outliers start: 24
  outliers final: 11
  residues processed: 124
  average time/residue: 0.9213
  time to fit residues: 123.6363
Evaluate side-chains
  121 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  297 ILE
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  356 ARG
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   84 ASN
Chi-restraints excluded: chain H residue  111 GLN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   77 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 59 optimal weight:    0.3980
   chunk 16 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 ASN
B 265 ASN
B 459 GLN
B 527 HIS
L  37 GLN
L  55 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.119179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.101620 restraints weight = 11207.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 1.45
r_work: 0.3368 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.3958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   7304  Z= 0.274
  Angle     :  0.632  10.621   9979  Z= 0.297
  Chirality :  0.043   0.206   1118
  Planarity :  0.004   0.048   1209
  Dihedral  :  8.485 163.476   1118
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 20.87 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.29), residues: 871
  helix:  1.32 (0.26), residues: 371
  sheet: -0.36 (0.36), residues: 204
  loop : -0.24 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 337 
 HIS   0.007   0.001   HIS B 115 
 PHE   0.022   0.002   PHE B 416 
 TYR   0.026   0.002   TYR B 201 
 ARG   0.007   0.001   ARG B 531 

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

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

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1742 Ramachandran restraints generated.
    871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.835 
Fit side-chains
REVERT: B  356 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7116 (mtt180)
REVERT: B  393 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7856 (p)
REVERT: B  402 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.5953 (tp30)
REVERT: B  465 MET cc_start: 0.7140 (mmt) cc_final: 0.6784 (mmm)
REVERT: H   49 MET cc_start: 0.8495 (mtp) cc_final: 0.8028 (ptm)
REVERT: H   84 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7538 (m-40)
REVERT: H  111 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.6557 (pm20)
REVERT: L   63 THR cc_start: 0.8005 (m) cc_final: 0.7700 (p)
  outliers start: 19
  outliers final: 9
  residues processed: 125
  average time/residue: 0.9737
  time to fit residues: 131.2297
Evaluate side-chains
  126 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  356 ARG
Chi-restraints excluded: chain B residue  393 THR
Chi-restraints excluded: chain B residue  402 GLU
Chi-restraints excluded: chain B residue  536 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   84 ASN
Chi-restraints excluded: chain H residue  111 GLN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   77 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 46 optimal weight:    0.5980
   chunk 17 optimal weight:    0.1980
   chunk 24 optimal weight:    0.7980
   chunk 53 optimal weight:    0.5980
   chunk 8 optimal weight:    0.1980
   chunk 6 optimal weight:    2.9990
   chunk 18 optimal weight:    0.2980
   chunk 16 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0170
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.2618

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 ASN
B 265 ASN
B 459 GLN
B 527 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.121378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.104189 restraints weight = 11095.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 1.44
r_work: 0.3412 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3296 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.4045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   7304  Z= 0.191
  Angle     :  0.601   8.792   9979  Z= 0.282
  Chirality :  0.042   0.159   1118
  Planarity :  0.004   0.050   1209
  Dihedral  :  8.350 160.055   1118
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 21.85 %
    Favored  : 75.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.29), residues: 871
  helix:  1.48 (0.27), residues: 367
  sheet: -0.40 (0.37), residues: 197
  loop : -0.19 (0.37), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 337 
 HIS   0.005   0.001   HIS B 115 
 PHE   0.020   0.001   PHE B 416 
 TYR   0.019   0.001   TYR B 201 
 ARG   0.003   0.000   ARG H  98 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5903.68 seconds
wall clock time: 104 minutes 10.32 seconds (6250.32 seconds total)