Starting phenix.real_space_refine
on Thu Jun 12 05:29:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tkt_25981/06_2025/7tkt_25981.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tkt_25981/06_2025/7tkt_25981.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tkt_25981/06_2025/7tkt_25981.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tkt_25981/06_2025/7tkt_25981.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tkt_25981/06_2025/7tkt_25981.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tkt_25981/06_2025/7tkt_25981.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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: 5
    Type Number    sf(0)   Gaussians
     P      12      5.49       5
     S      28      5.16       5
     C    8844      2.51       5
     N    2080      2.21       5
     O    2288      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 13252
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 390, 3103
          Classifications: {'peptide': 390}
          Link IDs: {'PTRANS': 23, 'TRANS': 366}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 3103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 390, 3103
          Classifications: {'peptide': 390}
          Link IDs: {'PTRANS': 23, 'TRANS': 366}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 210
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 210
          Unusual residues: {'PGW': 13}
          Classifications: {'RNA': 1, 'undetermined': 13}
          Modifications used: {'rna3p': 1}
          Link IDs: {None: 13}
          Unresolved non-hydrogen bonds: 475
          Unresolved non-hydrogen angles: 552
          Unresolved non-hydrogen dihedrals: 475
          Unresolved non-hydrogen chiralities: 22
          Planarities with less than four sites: {'PGW:plan-1': 11, 'PGW:plan-2': 11, 'PGW:plan-3': 10}
          Unresolved non-hydrogen planarities: 104
    Chain: "D"
      Number of atoms: 210
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 210
          Unusual residues: {'PGW': 13}
          Classifications: {'RNA': 1, 'undetermined': 13}
          Modifications used: {'rna3p': 1}
          Link IDs: {None: 13}
          Unresolved non-hydrogen bonds: 475
          Unresolved non-hydrogen angles: 552
          Unresolved non-hydrogen dihedrals: 475
          Unresolved non-hydrogen chiralities: 22
          Planarities with less than four sites: {'PGW:plan-1': 11, 'PGW:plan-2': 11, 'PGW:plan-3': 10}
          Unresolved non-hydrogen planarities: 104
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 8.24, per 1000 atoms: 0.62
  Number of scatterers: 13252
  At special positions: 0
  Unit cell: (105.226, 105.226, 122.763, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      28     16.00
     P      12     15.00
     O    2288      8.00
     N    2080      7.00
     C    8844      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 153 " - pdb=" SG  CYS B 153 " distance=0.00
    Simple disulfide: pdb=" SG  CYS B 387 " - pdb=" SG  CYS B 387 " distance=0.00

  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: 3.18
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2960

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 8 sheets defined
      63.3% alpha, 3.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 36
      Proline residue:  A  31  - end of helix
    Processing helix  chain 'A' and resid 44 through 56
    Processing helix  chain 'A' and resid 57 through 62
    Processing helix  chain 'A' and resid 81 through 89
      removed outlier: 4.009A  pdb=" N   LEU A  89 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 112
      removed outlier: 4.113A  pdb=" N   LEU A 106 " --> pdb=" O   PRO A 103 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LEU A 107 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER A 108 " --> pdb=" O   SER A 105 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL A 110 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   ARG A 111 " --> pdb=" O   SER A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 126
      removed outlier: 3.775A  pdb=" N   SER A 117 " --> pdb=" O   LEU A 113 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ARG A 124 " --> pdb=" O   ARG A 120 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU A 126 " --> pdb=" O   ALA A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 158
    Processing helix  chain 'A' and resid 165 through 182
    Processing helix  chain 'A' and resid 193 through 224
    Processing helix  chain 'A' and resid 227 through 246
      removed outlier: 3.555A  pdb=" N   ARG A 233 " --> pdb=" O   LYS A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 268
    Processing helix  chain 'A' and resid 271 through 276
    Processing helix  chain 'A' and resid 280 through 292
    Processing helix  chain 'A' and resid 306 through 315
      removed outlier: 4.108A  pdb=" N   ILE A 310 " --> pdb=" O   GLY A 306 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   LEU A 315 " --> pdb=" O   ARG A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 402
    Processing helix  chain 'A' and resid 404 through 416
      removed outlier: 3.855A  pdb=" N   LEU A 414 " --> pdb=" O   GLN A 410 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   VAL A 416 " --> pdb=" O   GLN A 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 36
      Proline residue:  B  31  - end of helix
    Processing helix  chain 'B' and resid 44 through 56
    Processing helix  chain 'B' and resid 57 through 62
    Processing helix  chain 'B' and resid 81 through 89
      removed outlier: 4.009A  pdb=" N   LEU B  89 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 112
      removed outlier: 4.113A  pdb=" N   LEU B 106 " --> pdb=" O   PRO B 103 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LEU B 107 " --> pdb=" O   LEU B 104 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER B 108 " --> pdb=" O   SER B 105 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL B 110 " --> pdb=" O   LEU B 107 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   ARG B 111 " --> pdb=" O   SER B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 126
      removed outlier: 3.775A  pdb=" N   SER B 117 " --> pdb=" O   LEU B 113 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   ARG B 124 " --> pdb=" O   ARG B 120 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU B 126 " --> pdb=" O   ALA B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 158
    Processing helix  chain 'B' and resid 165 through 182
    Processing helix  chain 'B' and resid 193 through 224
    Processing helix  chain 'B' and resid 227 through 246
      removed outlier: 3.555A  pdb=" N   ARG B 233 " --> pdb=" O   LYS B 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 268
    Processing helix  chain 'B' and resid 271 through 276
    Processing helix  chain 'B' and resid 280 through 292
    Processing helix  chain 'B' and resid 306 through 315
      removed outlier: 4.109A  pdb=" N   ILE B 310 " --> pdb=" O   GLY B 306 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   LEU B 315 " --> pdb=" O   ARG B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 402
    Processing helix  chain 'B' and resid 404 through 416
      removed outlier: 3.855A  pdb=" N   LEU B 414 " --> pdb=" O   GLN B 410 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   VAL B 416 " --> pdb=" O   GLN B 412 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 12 through 36
      Proline residue:  C  31  - end of helix
    Processing helix  chain 'C' and resid 44 through 56
    Processing helix  chain 'C' and resid 57 through 62
    Processing helix  chain 'C' and resid 81 through 89
      removed outlier: 4.010A  pdb=" N   LEU C  89 " --> pdb=" O   LEU C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 112
      removed outlier: 4.113A  pdb=" N   LEU C 106 " --> pdb=" O   PRO C 103 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LEU C 107 " --> pdb=" O   LEU C 104 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER C 108 " --> pdb=" O   SER C 105 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL C 110 " --> pdb=" O   LEU C 107 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   ARG C 111 " --> pdb=" O   SER C 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 126
      removed outlier: 3.775A  pdb=" N   SER C 117 " --> pdb=" O   LEU C 113 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ARG C 124 " --> pdb=" O   ARG C 120 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU C 126 " --> pdb=" O   ALA C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 131 through 158
    Processing helix  chain 'C' and resid 165 through 182
    Processing helix  chain 'C' and resid 193 through 224
    Processing helix  chain 'C' and resid 227 through 246
      removed outlier: 3.555A  pdb=" N   ARG C 233 " --> pdb=" O   LYS C 229 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 249 through 268
    Processing helix  chain 'C' and resid 271 through 276
    Processing helix  chain 'C' and resid 280 through 292
    Processing helix  chain 'C' and resid 306 through 315
      removed outlier: 4.107A  pdb=" N   ILE C 310 " --> pdb=" O   GLY C 306 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   LEU C 315 " --> pdb=" O   ARG C 311 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 394 through 402
    Processing helix  chain 'C' and resid 404 through 416
      removed outlier: 3.855A  pdb=" N   LEU C 414 " --> pdb=" O   GLN C 410 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   VAL C 416 " --> pdb=" O   GLN C 412 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 12 through 36
      Proline residue:  D  31  - end of helix
    Processing helix  chain 'D' and resid 44 through 56
    Processing helix  chain 'D' and resid 57 through 62
    Processing helix  chain 'D' and resid 81 through 89
      removed outlier: 4.009A  pdb=" N   LEU D  89 " --> pdb=" O   LEU D  85 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 102 through 112
      removed outlier: 4.113A  pdb=" N   LEU D 106 " --> pdb=" O   PRO D 103 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LEU D 107 " --> pdb=" O   LEU D 104 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   SER D 108 " --> pdb=" O   SER D 105 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL D 110 " --> pdb=" O   LEU D 107 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   ARG D 111 " --> pdb=" O   SER D 108 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 113 through 126
      removed outlier: 3.776A  pdb=" N   SER D 117 " --> pdb=" O   LEU D 113 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ARG D 124 " --> pdb=" O   ARG D 120 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU D 126 " --> pdb=" O   ALA D 122 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 131 through 158
    Processing helix  chain 'D' and resid 165 through 182
    Processing helix  chain 'D' and resid 193 through 224
    Processing helix  chain 'D' and resid 227 through 246
      removed outlier: 3.555A  pdb=" N   ARG D 233 " --> pdb=" O   LYS D 229 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 249 through 268
    Processing helix  chain 'D' and resid 271 through 276
    Processing helix  chain 'D' and resid 280 through 292
    Processing helix  chain 'D' and resid 306 through 315
      removed outlier: 4.107A  pdb=" N   ILE D 310 " --> pdb=" O   GLY D 306 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   LEU D 315 " --> pdb=" O   ARG D 311 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 394 through 402
    Processing helix  chain 'D' and resid 404 through 416
      removed outlier: 3.855A  pdb=" N   LEU D 414 " --> pdb=" O   GLN D 410 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   VAL D 416 " --> pdb=" O   GLN D 412 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 319
    Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329
      removed outlier: 6.747A  pdb=" N   TYR A 327 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   ALA A 383 " --> pdb=" O   TYR A 327 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ALA A 358 " --> pdb=" O   VAL A 348 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 318 through 319
    Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329
      removed outlier: 6.747A  pdb=" N   TYR B 327 " --> pdb=" O   ALA B 383 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   ALA B 383 " --> pdb=" O   TYR B 327 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ALA B 358 " --> pdb=" O   VAL B 348 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 318 through 319
    Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329
      removed outlier: 6.747A  pdb=" N   TYR C 327 " --> pdb=" O   ALA C 383 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   ALA C 383 " --> pdb=" O   TYR C 327 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ALA C 358 " --> pdb=" O   VAL C 348 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 319
    Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329
      removed outlier: 6.747A  pdb=" N   TYR D 327 " --> pdb=" O   ALA D 383 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   ALA D 383 " --> pdb=" O   TYR D 327 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ALA D 358 " --> pdb=" O   VAL D 348 " (cutoff:3.500A)

    728 hydrogen bonds defined for protein.
    2088 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: 3.26

  Time building geometry restraints manager: 3.71 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3845
        1.34 -     1.45: 1694
        1.45 -     1.57: 7881
        1.57 -     1.69: 16
        1.69 -     1.81: 56
  Bond restraints: 13492
  Sorted by residual:
  bond pdb=" C10 PGW B 513 "
       pdb=" C9  PGW B 513 "
    ideal  model  delta    sigma   weight residual
    1.333  1.504 -0.171 2.00e-02 2.50e+03 7.33e+01
  bond pdb=" C10 PGW D 502 "
       pdb=" C9  PGW D 502 "
    ideal  model  delta    sigma   weight residual
    1.333  1.504 -0.171 2.00e-02 2.50e+03 7.29e+01
  bond pdb=" C10 PGW B 510 "
       pdb=" C9  PGW B 510 "
    ideal  model  delta    sigma   weight residual
    1.333  1.504 -0.171 2.00e-02 2.50e+03 7.29e+01
  bond pdb=" C10 PGW C 510 "
       pdb=" C9  PGW C 510 "
    ideal  model  delta    sigma   weight residual
    1.333  1.504 -0.171 2.00e-02 2.50e+03 7.29e+01
  bond pdb=" C10 PGW A 510 "
       pdb=" C9  PGW A 510 "
    ideal  model  delta    sigma   weight residual
    1.333  1.504 -0.171 2.00e-02 2.50e+03 7.29e+01
  ... (remaining 13487 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.21: 17753
        4.21 -     8.43: 379
        8.43 -    12.64: 8
       12.64 -    16.86: 0
       16.86 -    21.07: 16
  Bond angle restraints: 18156
  Sorted by residual:
  angle pdb=" C10 PGW B 513 "
        pdb=" C9  PGW B 513 "
        pdb=" C8  PGW B 513 "
      ideal   model   delta    sigma   weight residual
     127.02  105.95   21.07 3.00e+00 1.11e-01 4.93e+01
  angle pdb=" C10 PGW D 505 "
        pdb=" C9  PGW D 505 "
        pdb=" C8  PGW D 505 "
      ideal   model   delta    sigma   weight residual
     127.02  105.96   21.06 3.00e+00 1.11e-01 4.93e+01
  angle pdb=" C10 PGW C 513 "
        pdb=" C9  PGW C 513 "
        pdb=" C8  PGW C 513 "
      ideal   model   delta    sigma   weight residual
     127.02  105.96   21.06 3.00e+00 1.11e-01 4.93e+01
  angle pdb=" C10 PGW A 513 "
        pdb=" C9  PGW A 513 "
        pdb=" C8  PGW A 513 "
      ideal   model   delta    sigma   weight residual
     127.02  105.96   21.06 3.00e+00 1.11e-01 4.93e+01
  angle pdb=" C10 PGW C 510 "
        pdb=" C9  PGW C 510 "
        pdb=" C8  PGW C 510 "
      ideal   model   delta    sigma   weight residual
     127.02  106.26   20.76 3.00e+00 1.11e-01 4.79e+01
  ... (remaining 18151 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.68: 7976
       34.68 -    69.36: 208
       69.36 -   104.04: 52
      104.04 -   138.71: 12
      138.71 -   173.39: 32
  Dihedral angle restraints: 8280
    sinusoidal: 3692
      harmonic: 4588
  Sorted by residual:
  dihedral pdb=" C3' CMP C 501 "
           pdb=" O3' CMP C 501 "
           pdb=" P   CMP C 501 "
           pdb=" O1P CMP C 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  100.95 -160.95     1      2.00e+01 2.50e-03 4.67e+01
  dihedral pdb=" C3' CMP D 507 "
           pdb=" O3' CMP D 507 "
           pdb=" P   CMP D 507 "
           pdb=" O1P CMP D 507 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  100.94 -160.94     1      2.00e+01 2.50e-03 4.67e+01
  dihedral pdb=" C3' CMP A 501 "
           pdb=" O3' CMP A 501 "
           pdb=" P   CMP A 501 "
           pdb=" O1P CMP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  100.94 -160.94     1      2.00e+01 2.50e-03 4.67e+01
  ... (remaining 8277 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1311
       0.034 -    0.069: 547
       0.069 -    0.103: 191
       0.103 -    0.137: 39
       0.137 -    0.171: 12
  Chirality restraints: 2100
  Sorted by residual:
  chirality pdb=" C02 PGW C 503 "
            pdb=" C01 PGW C 503 "
            pdb=" C03 PGW C 503 "
            pdb=" O01 PGW C 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.36    2.53   -0.17 2.00e-01 2.50e+01 7.35e-01
  chirality pdb=" C02 PGW D 509 "
            pdb=" C01 PGW D 509 "
            pdb=" C03 PGW D 509 "
            pdb=" O01 PGW D 509 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.36    2.53   -0.17 2.00e-01 2.50e+01 7.35e-01
  chirality pdb=" CA  GLN D 412 "
            pdb=" N   GLN D 412 "
            pdb=" C   GLN D 412 "
            pdb=" CB  GLN D 412 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.31e-01
  ... (remaining 2097 not shown)

  Planarity restraints: 2172
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C06 PGW B 513 "   -0.159 2.00e-02 2.50e+03   1.59e-01 2.52e+02
        pdb=" C10 PGW B 513 "    0.161 2.00e-02 2.50e+03
        pdb=" C8  PGW B 513 "   -0.158 2.00e-02 2.50e+03
        pdb=" C9  PGW B 513 "    0.156 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C06 PGW D 505 "    0.159 2.00e-02 2.50e+03   1.59e-01 2.52e+02
        pdb=" C10 PGW D 505 "   -0.161 2.00e-02 2.50e+03
        pdb=" C8  PGW D 505 "    0.158 2.00e-02 2.50e+03
        pdb=" C9  PGW D 505 "   -0.156 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C06 PGW C 513 "    0.159 2.00e-02 2.50e+03   1.59e-01 2.52e+02
        pdb=" C10 PGW C 513 "   -0.161 2.00e-02 2.50e+03
        pdb=" C8  PGW C 513 "    0.158 2.00e-02 2.50e+03
        pdb=" C9  PGW C 513 "   -0.156 2.00e-02 2.50e+03
  ... (remaining 2169 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1950
        2.76 -     3.29: 12129
        3.29 -     3.83: 21391
        3.83 -     4.36: 22528
        4.36 -     4.90: 40837
  Nonbonded interactions: 98835
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 180 "
            pdb=" OH  TYR D 186 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OH  TYR A 186 "
            pdb=" OG1 THR B 180 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OH  TYR B 186 "
            pdb=" OG1 THR C 180 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OH  TYR C 186 "
            pdb=" OG1 THR D 180 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OH  TYR B 262 "
            pdb=" OD2 ASP B 388 "
     model   vdw
     2.264 3.040
  ... (remaining 98830 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: 0.09
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 10 through 416 or (resid 502 and (name C06 or name C07 or  \ 
name C08 or name C09 or name C1 or name C10 or name C11 or name C12 or name C2 o \ 
r name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) o \ 
r resid 504 through 505 or resid 508 through 509 or (resid 510 through 511 and ( \ 
name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 513  \ 
through 514 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6  \ 
))))
  selection = (chain 'B' and (resid 10 through 416 or (resid 502 and (name C06 or name C07 or  \ 
name C08 or name C09 or name C1 or name C10 or name C11 or name C12 or name C2 o \ 
r name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) o \ 
r resid 504 through 505 or resid 508 through 509 or (resid 510 through 511 and ( \ 
name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 513  \ 
through 514 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6  \ 
))))
  selection = (chain 'C' and (resid 10 through 416 or (resid 502 and (name C06 or name C07 or  \ 
name C08 or name C09 or name C1 or name C10 or name C11 or name C12 or name C2 o \ 
r name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) o \ 
r resid 504 through 505 or resid 508 through 509 or (resid 510 through 511 and ( \ 
name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 513  \ 
through 514 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6  \ 
))))
  selection = (chain 'D' and (resid 10 through 416 or resid 502 or (resid 504 through 505 and  \ 
(name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 508 \ 
 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resi \ 
d 509 and (name C15 or name C16 or name C17 or name C18 or name C19 or name C20  \ 
or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name  \ 
C27 or name C28)) or resid 510 through 511 or resid 513 through 514))
}

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 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:             0.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     29.710
  Find NCS groups from input model:        0.680
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
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      :  0.007   0.171  13492  Z= 0.327
  Angle     :  1.264  21.069  18158  Z= 0.478
  Chirality :  0.044   0.171   2100
  Planarity :  0.008   0.159   2172
  Dihedral  : 21.053 173.393   5316
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.22), residues: 1544
  helix:  1.56 (0.18), residues: 936
  sheet:  0.59 (0.57), residues: 84
  loop : -1.78 (0.26), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 264 
 HIS   0.002   0.001   HIS C 292 
 PHE   0.005   0.001   PHE D 386 
 TYR   0.009   0.001   TYR B  26 
 ARG   0.001   0.000   ARG D 311 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12057 (  728)
  hydrogen bonds       : angle       5.41712 ( 2088)
  SS BOND              : angle       0.00000 (    2)
  covalent geometry    : bond        0.00659 (13492)
  covalent geometry    : angle       1.26412 (18156)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 1.378 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.2508
  time to fit residues: 55.8988
Evaluate side-chains
  125 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 1.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    0.7980
   chunk 118 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 79 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 122 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 141 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 217 ASN
B 217 ASN
C 217 ASN
D 217 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.157068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.123752 restraints weight = 21024.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.123525 restraints weight = 15824.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.123979 restraints weight = 13985.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.1021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13492  Z= 0.132
  Angle     :  0.620   9.100  18158  Z= 0.289
  Chirality :  0.041   0.132   2100
  Planarity :  0.004   0.042   2172
  Dihedral  : 21.069 163.068   2372
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  7.61 %
    Favored  : 92.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.23), residues: 1544
  helix:  1.93 (0.18), residues: 928
  sheet: -0.65 (0.41), residues: 156
  loop : -1.94 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 176 
 HIS   0.003   0.001   HIS A 149 
 PHE   0.012   0.001   PHE D  40 
 TYR   0.013   0.001   TYR D  25 
 ARG   0.002   0.000   ARG C 382 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03731 (  728)
  hydrogen bonds       : angle       4.12998 ( 2088)
  SS BOND              : angle       0.00000 (    2)
  covalent geometry    : bond        0.00300 (13492)
  covalent geometry    : angle       0.62040 (18156)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 122
  time to evaluate  : 1.545 
Fit side-chains
REVERT: A   82 LEU cc_start: 0.7433 (tt) cc_final: 0.6702 (mp)
REVERT: B   57 ASP cc_start: 0.5581 (t0) cc_final: 0.5180 (p0)
REVERT: B   82 LEU cc_start: 0.7429 (tt) cc_final: 0.6692 (mp)
REVERT: C   82 LEU cc_start: 0.7422 (tt) cc_final: 0.6706 (mp)
REVERT: D   82 LEU cc_start: 0.7424 (tt) cc_final: 0.6708 (mp)
REVERT: D  369 MET cc_start: 0.7664 (tpp) cc_final: 0.7453 (tpt)
  outliers start: 4
  outliers final: 0
  residues processed: 126
  average time/residue: 0.2440
  time to fit residues: 46.5578
Evaluate side-chains
  115 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 1.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 142 optimal weight:    0.7980
   chunk 136 optimal weight:    0.4980
   chunk 87 optimal weight:    2.9990
   chunk 101 optimal weight:    0.6980
   chunk 107 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 148 optimal weight:    6.9990
   chunk 94 optimal weight:    4.9990
   chunk 59 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.158235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.124484 restraints weight = 21419.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.123845 restraints weight = 16061.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.125039 restraints weight = 13970.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.1348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13492  Z= 0.114
  Angle     :  0.594   8.998  18158  Z= 0.274
  Chirality :  0.041   0.138   2100
  Planarity :  0.004   0.039   2172
  Dihedral  : 18.240 163.355   2372
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 12.84 %
    Favored  : 86.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.23), residues: 1544
  helix:  2.05 (0.18), residues: 928
  sheet: -0.82 (0.41), residues: 156
  loop : -1.71 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 176 
 HIS   0.002   0.000   HIS B 149 
 PHE   0.039   0.001   PHE A  40 
 TYR   0.010   0.001   TYR D  26 
 ARG   0.002   0.000   ARG D 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03334 (  728)
  hydrogen bonds       : angle       3.78582 ( 2088)
  SS BOND              : angle       0.00000 (    2)
  covalent geometry    : bond        0.00255 (13492)
  covalent geometry    : angle       0.59422 (18156)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 141
  time to evaluate  : 1.312 
Fit side-chains
REVERT: A   82 LEU cc_start: 0.7398 (tt) cc_final: 0.6725 (mp)
REVERT: B   82 LEU cc_start: 0.7379 (tt) cc_final: 0.6725 (mp)
REVERT: C   82 LEU cc_start: 0.7383 (tt) cc_final: 0.6728 (mp)
REVERT: D   82 LEU cc_start: 0.7386 (tt) cc_final: 0.6728 (mp)
REVERT: D  369 MET cc_start: 0.7732 (tpp) cc_final: 0.7531 (tpt)
  outliers start: 8
  outliers final: 0
  residues processed: 145
  average time/residue: 0.2188
  time to fit residues: 48.3997
Evaluate side-chains
  125 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 1.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 55 optimal weight:    7.9990
   chunk 71 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 141 optimal weight:    3.9990
   chunk 119 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   chunk 143 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 39 optimal weight:   10.0000
   overall best weight:    2.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.151507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.117831 restraints weight = 21200.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.117794 restraints weight = 18288.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.118732 restraints weight = 15410.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  13492  Z= 0.205
  Angle     :  0.657   8.290  18158  Z= 0.316
  Chirality :  0.043   0.135   2100
  Planarity :  0.004   0.037   2172
  Dihedral  : 17.540 162.509   2372
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 17.54 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.23), residues: 1544
  helix:  1.89 (0.18), residues: 928
  sheet: -0.62 (0.44), residues: 128
  loop : -1.78 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 176 
 HIS   0.004   0.001   HIS D 149 
 PHE   0.037   0.002   PHE A  40 
 TYR   0.013   0.001   TYR D  26 
 ARG   0.003   0.000   ARG A 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04255 (  728)
  hydrogen bonds       : angle       3.95137 ( 2088)
  SS BOND              : angle       0.00000 (    2)
  covalent geometry    : bond        0.00495 (13492)
  covalent geometry    : angle       0.65723 (18156)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 138
  time to evaluate  : 1.366 
Fit side-chains
REVERT: A   82 LEU cc_start: 0.7507 (tt) cc_final: 0.6817 (mp)
REVERT: B   82 LEU cc_start: 0.7442 (tt) cc_final: 0.6750 (mp)
REVERT: B   96 PHE cc_start: 0.6605 (m-80) cc_final: 0.6349 (m-10)
REVERT: C   82 LEU cc_start: 0.7444 (tt) cc_final: 0.6748 (mp)
REVERT: C   96 PHE cc_start: 0.6719 (m-80) cc_final: 0.6468 (m-10)
REVERT: D   82 LEU cc_start: 0.7449 (tt) cc_final: 0.6752 (mp)
REVERT: D   96 PHE cc_start: 0.6721 (m-80) cc_final: 0.6471 (m-10)
  outliers start: 5
  outliers final: 0
  residues processed: 139
  average time/residue: 0.2611
  time to fit residues: 52.6892
Evaluate side-chains
  121 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 1.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 83 optimal weight:    9.9990
   chunk 72 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 136 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 142 optimal weight:    0.0770
   chunk 139 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.6738

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.155313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.117531 restraints weight = 21584.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.120395 restraints weight = 14240.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.122371 restraints weight = 11080.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13492  Z= 0.118
  Angle     :  0.603  10.151  18158  Z= 0.284
  Chirality :  0.041   0.128   2100
  Planarity :  0.004   0.037   2172
  Dihedral  : 16.775 163.354   2372
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 18.96 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.23), residues: 1544
  helix:  1.91 (0.18), residues: 924
  sheet: -0.70 (0.44), residues: 128
  loop : -1.79 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 176 
 HIS   0.001   0.000   HIS D  99 
 PHE   0.040   0.001   PHE A  40 
 TYR   0.006   0.001   TYR A 128 
 ARG   0.001   0.000   ARG B 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03415 (  728)
  hydrogen bonds       : angle       3.74686 ( 2088)
  SS BOND              : angle       0.00000 (    2)
  covalent geometry    : bond        0.00266 (13492)
  covalent geometry    : angle       0.60302 (18156)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 1.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 LEU cc_start: 0.7439 (tt) cc_final: 0.6826 (mp)
REVERT: B   82 LEU cc_start: 0.7360 (tt) cc_final: 0.6769 (mp)
REVERT: B   96 PHE cc_start: 0.6964 (m-80) cc_final: 0.6673 (m-10)
REVERT: C   82 LEU cc_start: 0.7366 (tt) cc_final: 0.6744 (mp)
REVERT: C   96 PHE cc_start: 0.6945 (m-80) cc_final: 0.6668 (m-10)
REVERT: D   82 LEU cc_start: 0.7371 (tt) cc_final: 0.6745 (mp)
  outliers start: 12
  outliers final: 0
  residues processed: 146
  average time/residue: 0.2438
  time to fit residues: 52.0005
Evaluate side-chains
  127 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 13 optimal weight:    0.1980
   chunk 23 optimal weight:    0.7980
   chunk 64 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 123 optimal weight:    8.9990
   chunk 112 optimal weight:    0.9990
   chunk 142 optimal weight:    0.9980
   chunk 149 optimal weight:    5.9990
   chunk 5 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.155832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.118146 restraints weight = 21643.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.121097 restraints weight = 14150.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.122984 restraints weight = 11005.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13492  Z= 0.116
  Angle     :  0.602   9.538  18158  Z= 0.282
  Chirality :  0.041   0.134   2100
  Planarity :  0.004   0.036   2172
  Dihedral  : 16.469 163.851   2372
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 20.37 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.23), residues: 1544
  helix:  1.99 (0.18), residues: 924
  sheet: -0.68 (0.45), residues: 128
  loop : -1.77 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 176 
 HIS   0.002   0.001   HIS A 149 
 PHE   0.040   0.001   PHE A  40 
 TYR   0.005   0.001   TYR A 128 
 ARG   0.001   0.000   ARG A 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03285 (  728)
  hydrogen bonds       : angle       3.66133 ( 2088)
  SS BOND              : angle       0.00000 (    2)
  covalent geometry    : bond        0.00262 (13492)
  covalent geometry    : angle       0.60170 (18156)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 130
  time to evaluate  : 1.536 
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: A   82 LEU cc_start: 0.7438 (tt) cc_final: 0.6828 (mp)
REVERT: B   82 LEU cc_start: 0.7360 (tt) cc_final: 0.6776 (mp)
REVERT: B   96 PHE cc_start: 0.6868 (m-80) cc_final: 0.6571 (m-10)
REVERT: C   82 LEU cc_start: 0.7360 (tt) cc_final: 0.6752 (mp)
REVERT: C   96 PHE cc_start: 0.6939 (m-80) cc_final: 0.6648 (m-10)
REVERT: D   82 LEU cc_start: 0.7367 (tt) cc_final: 0.6753 (mp)
REVERT: D   96 PHE cc_start: 0.7522 (m-80) cc_final: 0.7202 (m-10)
  outliers start: 5
  outliers final: 1
  residues processed: 135
  average time/residue: 0.2859
  time to fit residues: 56.4069
Evaluate side-chains
  130 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 1.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 24 optimal weight:    0.2980
   chunk 121 optimal weight:    8.9990
   chunk 75 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 44 optimal weight:    8.9990
   chunk 11 optimal weight:    6.9990
   chunk 85 optimal weight:    0.0980
   chunk 56 optimal weight:    2.9990
   chunk 136 optimal weight:    0.9990
   chunk 110 optimal weight:    4.9990
   overall best weight:    1.0786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.154731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.116862 restraints weight = 21596.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.119815 restraints weight = 14105.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.121777 restraints weight = 10954.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.2076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13492  Z= 0.136
  Angle     :  0.628   9.426  18158  Z= 0.294
  Chirality :  0.042   0.139   2100
  Planarity :  0.004   0.035   2172
  Dihedral  : 16.392 163.487   2372
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  : 21.79 %
    Favored  : 78.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.23), residues: 1544
  helix:  1.93 (0.18), residues: 924
  sheet: -0.66 (0.45), residues: 128
  loop : -1.77 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 176 
 HIS   0.002   0.001   HIS C 149 
 PHE   0.042   0.001   PHE A  40 
 TYR   0.007   0.001   TYR D 175 
 ARG   0.002   0.000   ARG D 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03443 (  728)
  hydrogen bonds       : angle       3.68583 ( 2088)
  SS BOND              : angle       0.00000 (    2)
  covalent geometry    : bond        0.00321 (13492)
  covalent geometry    : angle       0.62786 (18156)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 1.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 LEU cc_start: 0.7437 (tt) cc_final: 0.6827 (mp)
REVERT: B   82 LEU cc_start: 0.7364 (tt) cc_final: 0.6774 (mp)
REVERT: B   96 PHE cc_start: 0.6897 (m-80) cc_final: 0.6616 (m-10)
REVERT: C   82 LEU cc_start: 0.7435 (tt) cc_final: 0.6824 (mp)
REVERT: C   96 PHE cc_start: 0.6848 (m-80) cc_final: 0.6570 (m-10)
REVERT: D   82 LEU cc_start: 0.7438 (tt) cc_final: 0.6824 (mp)
REVERT: D   96 PHE cc_start: 0.7551 (m-80) cc_final: 0.7269 (m-10)
  outliers start: 1
  outliers final: 1
  residues processed: 136
  average time/residue: 0.2634
  time to fit residues: 52.1615
Evaluate side-chains
  137 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 1.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 116 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 125 optimal weight:    0.9990
   chunk 144 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 143 optimal weight:    0.9980
   chunk 115 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0470
   overall best weight:    0.5878

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.156432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.119428 restraints weight = 21433.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.122253 restraints weight = 14376.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.123999 restraints weight = 11269.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13492  Z= 0.114
  Angle     :  0.614   9.597  18158  Z= 0.287
  Chirality :  0.042   0.141   2100
  Planarity :  0.004   0.035   2172
  Dihedral  : 16.164 163.942   2372
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 21.34 %
    Favored  : 77.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.23), residues: 1544
  helix:  1.96 (0.18), residues: 924
  sheet: -0.52 (0.54), residues: 92
  loop : -1.51 (0.28), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 176 
 HIS   0.001   0.000   HIS A 149 
 PHE   0.044   0.001   PHE A  40 
 TYR   0.005   0.001   TYR A 128 
 ARG   0.001   0.000   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03198 (  728)
  hydrogen bonds       : angle       3.62400 ( 2088)
  SS BOND              : angle       0.00000 (    2)
  covalent geometry    : bond        0.00256 (13492)
  covalent geometry    : angle       0.61450 (18156)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 145
  time to evaluate  : 1.818 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 LEU cc_start: 0.7450 (tt) cc_final: 0.6825 (mp)
REVERT: B   82 LEU cc_start: 0.7378 (tt) cc_final: 0.6768 (mp)
REVERT: C   82 LEU cc_start: 0.7379 (tt) cc_final: 0.6752 (mp)
REVERT: C   96 PHE cc_start: 0.6723 (m-80) cc_final: 0.6465 (m-10)
REVERT: D   82 LEU cc_start: 0.7384 (tt) cc_final: 0.6751 (mp)
REVERT: D   96 PHE cc_start: 0.7532 (m-80) cc_final: 0.7273 (m-10)
  outliers start: 14
  outliers final: 2
  residues processed: 154
  average time/residue: 0.2537
  time to fit residues: 57.0051
Evaluate side-chains
  136 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 134
  time to evaluate  : 1.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  156 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 30 optimal weight:    7.9990
   chunk 108 optimal weight:    7.9990
   chunk 102 optimal weight:    0.8980
   chunk 155 optimal weight:    0.2980
   chunk 143 optimal weight:    0.7980
   chunk 113 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 153 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 412 GLN
D 412 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.156217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.122447 restraints weight = 21019.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.122504 restraints weight = 15525.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.122821 restraints weight = 12661.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13492  Z= 0.126
  Angle     :  0.648  11.579  18158  Z= 0.301
  Chirality :  0.043   0.209   2100
  Planarity :  0.004   0.038   2172
  Dihedral  : 16.095 163.689   2372
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 21.94 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.23), residues: 1544
  helix:  1.93 (0.18), residues: 924
  sheet: -0.39 (0.55), residues: 92
  loop : -1.51 (0.28), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 176 
 HIS   0.002   0.000   HIS D 149 
 PHE   0.045   0.001   PHE A  40 
 TYR   0.005   0.001   TYR A 128 
 ARG   0.002   0.000   ARG C 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03330 (  728)
  hydrogen bonds       : angle       3.67174 ( 2088)
  SS BOND              : angle       0.00000 (    2)
  covalent geometry    : bond        0.00292 (13492)
  covalent geometry    : angle       0.64845 (18156)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 135
  time to evaluate  : 1.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 LEU cc_start: 0.7422 (tt) cc_final: 0.6773 (mp)
REVERT: A  374 ARG cc_start: 0.7536 (mmm160) cc_final: 0.6988 (tpt90)
REVERT: B   82 LEU cc_start: 0.7350 (tt) cc_final: 0.6718 (mp)
REVERT: B  374 ARG cc_start: 0.7482 (mmm160) cc_final: 0.6947 (tpt90)
REVERT: C   82 LEU cc_start: 0.7549 (tt) cc_final: 0.6908 (mp)
REVERT: C  374 ARG cc_start: 0.7512 (mmm160) cc_final: 0.6955 (tpt90)
REVERT: D   82 LEU cc_start: 0.7548 (tt) cc_final: 0.6905 (mp)
REVERT: D   96 PHE cc_start: 0.7510 (m-80) cc_final: 0.7298 (m-10)
  outliers start: 7
  outliers final: 0
  residues processed: 141
  average time/residue: 0.2662
  time to fit residues: 54.8296
Evaluate side-chains
  135 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 1.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 29 optimal weight:    0.0670
   chunk 8 optimal weight:   10.0000
   chunk 42 optimal weight:    0.5980
   chunk 146 optimal weight:    0.0170
   chunk 73 optimal weight:    0.1980
   chunk 139 optimal weight:    1.9990
   chunk 109 optimal weight:    5.9990
   chunk 72 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 155 optimal weight:    9.9990
   overall best weight:    0.3156

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.158335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.124289 restraints weight = 21038.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.124440 restraints weight = 16334.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.125465 restraints weight = 14283.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.2224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13492  Z= 0.116
  Angle     :  0.673  10.849  18158  Z= 0.309
  Chirality :  0.043   0.176   2100
  Planarity :  0.004   0.037   2172
  Dihedral  : 15.907 163.946   2372
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.36 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.23), residues: 1544
  helix:  1.93 (0.18), residues: 924
  sheet: -0.24 (0.56), residues: 92
  loop : -1.45 (0.29), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 176 
 HIS   0.001   0.000   HIS D  99 
 PHE   0.045   0.001   PHE A  40 
 TYR   0.005   0.001   TYR A 199 
 ARG   0.002   0.000   ARG A 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03150 (  728)
  hydrogen bonds       : angle       3.63468 ( 2088)
  SS BOND              : angle       0.00000 (    2)
  covalent geometry    : bond        0.00254 (13492)
  covalent geometry    : angle       0.67257 (18156)

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

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

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3088 Ramachandran restraints generated.
    1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.322 
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: A   82 LEU cc_start: 0.7436 (tt) cc_final: 0.6742 (mp)
REVERT: B   82 LEU cc_start: 0.7364 (tt) cc_final: 0.6683 (mp)
REVERT: C   82 LEU cc_start: 0.7429 (tt) cc_final: 0.6740 (mp)
REVERT: D   82 LEU cc_start: 0.7428 (tt) cc_final: 0.6738 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.2621
  time to fit residues: 53.0192
Evaluate side-chains
  125 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 1.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 116 optimal weight:    5.9990
   chunk 109 optimal weight:    5.9990
   chunk 70 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0870
   chunk 69 optimal weight:    6.9990
   chunk 133 optimal weight:    3.9990
   chunk 112 optimal weight:    0.1980
   chunk 132 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 115 optimal weight:    0.9990
   chunk 88 optimal weight:    3.9990
   overall best weight:    0.9962

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.156060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.122606 restraints weight = 21172.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.122885 restraints weight = 16750.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.122705 restraints weight = 12402.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13492  Z= 0.137
  Angle     :  0.689  10.973  18158  Z= 0.317
  Chirality :  0.044   0.200   2100
  Planarity :  0.004   0.057   2172
  Dihedral  : 15.922 163.267   2372
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 23.21 %
    Favored  : 76.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.23), residues: 1544
  helix:  1.94 (0.18), residues: 924
  sheet: -0.24 (0.56), residues: 92
  loop : -1.38 (0.29), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 176 
 HIS   0.002   0.001   HIS A 149 
 PHE   0.065   0.002   PHE A  40 
 TYR   0.008   0.001   TYR D 327 
 ARG   0.007   0.000   ARG D 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03430 (  728)
  hydrogen bonds       : angle       3.67979 ( 2088)
  SS BOND              : angle       0.00000 (    2)
  covalent geometry    : bond        0.00321 (13492)
  covalent geometry    : angle       0.68898 (18156)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3671.08 seconds
wall clock time: 64 minutes 47.46 seconds (3887.46 seconds total)