Starting phenix.real_space_refine
on Tue Jul 29 15:34:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5k10_8192/07_2025/5k10_8192.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5k10_8192/07_2025/5k10_8192.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5k10_8192/07_2025/5k10_8192.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5k10_8192/07_2025/5k10_8192.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5k10_8192/07_2025/5k10_8192.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5k10_8192/07_2025/5k10_8192.cif"
  }
  resolution = 3.8
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 6334 atoms to isotropic.
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       6      5.49       5
     S      38      5.16       5
     C    4016      2.51       5
     N    1074      2.21       5
     O    1204      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6338
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 397, 3121
          Classifications: {'peptide': 397}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 12, 'TRANS': 384}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "A"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 48
          Unusual residues: {'NDP': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 7.14, per 1000 atoms: 1.13
  Number of scatterers: 6338
  At special positions: 0
  Unit cell: (99.495, 76.725, 82.665, 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      38     16.00
     P       6     15.00
     O    1204      8.00
     N    1074      7.00
     C    4016      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.51
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1464

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 8 sheets defined
      46.6% alpha, 13.6% 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 16 through 31
      removed outlier: 4.085A  pdb=" N   ILE A  21 " --> pdb=" O   GLU A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 49
    Processing helix  chain 'A' and resid 54 through 68
      removed outlier: 3.807A  pdb=" N   LYS A  58 " --> pdb=" O   ASP A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 86
      removed outlier: 3.754A  pdb=" N   GLU A  84 " --> pdb=" O   GLU A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 104
      removed outlier: 3.922A  pdb=" N   ILE A 102 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 204
    Processing helix  chain 'A' and resid 216 through 234
      removed outlier: 3.625A  pdb=" N   ASP A 220 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   PHE A 223 " --> pdb=" O   TYR A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 241
    Processing helix  chain 'A' and resid 242 through 244
      No H-bonds generated for 'chain 'A' and resid 242 through 244'
    Processing helix  chain 'A' and resid 251 through 260
      removed outlier: 4.414A  pdb=" N   GLN A 257 " --> pdb=" O   ASP A 253 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   MET A 259 " --> pdb=" O   VAL A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 348
      removed outlier: 3.574A  pdb=" N   TRP A 336 " --> pdb=" O   SER A 332 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LEU A 346 " --> pdb=" O   HIS A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 369
      removed outlier: 3.573A  pdb=" N   ALA A 353 " --> pdb=" O   ASN A 349 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLU A 361 " --> pdb=" O   ASN A 357 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   ILE A 367 " --> pdb=" O   SER A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 381
      removed outlier: 3.769A  pdb=" N   LYS A 381 " --> pdb=" O   ALA A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 391
    Processing helix  chain 'A' and resid 396 through 411
      removed outlier: 3.889A  pdb=" N   LYS A 400 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LEU A 401 " --> pdb=" O   PHE A 397 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLY A 402 " --> pdb=" O   MET A 398 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 31
      removed outlier: 4.086A  pdb=" N   ILE B  21 " --> pdb=" O   GLU B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 49
    Processing helix  chain 'B' and resid 54 through 68
      removed outlier: 3.808A  pdb=" N   LYS B  58 " --> pdb=" O   ASP B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 86
      removed outlier: 3.754A  pdb=" N   GLU B  84 " --> pdb=" O   GLU B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 104
      removed outlier: 3.922A  pdb=" N   ILE B 102 " --> pdb=" O   THR B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 204
    Processing helix  chain 'B' and resid 216 through 234
      removed outlier: 3.625A  pdb=" N   ASP B 220 " --> pdb=" O   LEU B 216 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   PHE B 223 " --> pdb=" O   TYR B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 241
    Processing helix  chain 'B' and resid 242 through 244
      No H-bonds generated for 'chain 'B' and resid 242 through 244'
    Processing helix  chain 'B' and resid 251 through 260
      removed outlier: 4.414A  pdb=" N   GLN B 257 " --> pdb=" O   ASP B 253 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   MET B 259 " --> pdb=" O   VAL B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 348
      removed outlier: 3.574A  pdb=" N   TRP B 336 " --> pdb=" O   SER B 332 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LEU B 346 " --> pdb=" O   HIS B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 369
      removed outlier: 3.573A  pdb=" N   ALA B 353 " --> pdb=" O   ASN B 349 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLU B 361 " --> pdb=" O   ASN B 357 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   ILE B 367 " --> pdb=" O   SER B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 381
      removed outlier: 3.768A  pdb=" N   LYS B 381 " --> pdb=" O   ALA B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 391
    Processing helix  chain 'B' and resid 396 through 411
      removed outlier: 3.888A  pdb=" N   LYS B 400 " --> pdb=" O   GLU B 396 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LEU B 401 " --> pdb=" O   PHE B 397 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLY B 402 " --> pdb=" O   MET B 398 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 9
      removed outlier: 4.272A  pdb=" N   SER A   6 " --> pdb=" O   GLU A  36 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   ASP A  38 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   GLY A   8 " --> pdb=" O   ASP A  38 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 14
    Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 72
      removed outlier: 3.782A  pdb=" N   ALA A 307 " --> pdb=" O   LYS A  72 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   VAL A 107 " --> pdb=" O   CYS A 132 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   CYS A 132 " --> pdb=" O   VAL A 107 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   ILE A 129 " --> pdb=" O   TRP A 267 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   CYS A 269 " --> pdb=" O   ILE A 129 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   GLY A 131 " --> pdb=" O   CYS A 269 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   ARG A 249 " --> pdb=" O   LEU A 207 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   LEU A 209 " --> pdb=" O   ARG A 249 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 144
    Processing sheet with id=AA5, first strand: chain 'A' and resid 171 through 172
    Processing sheet with id=AA6, first strand: chain 'B' and resid 5 through 9
      removed outlier: 4.272A  pdb=" N   SER B   6 " --> pdb=" O   GLU B  36 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   ASP B  38 " --> pdb=" O   SER B   6 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   GLY B   8 " --> pdb=" O   ASP B  38 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 14
    Processing sheet with id=AA8, first strand: chain 'B' and resid 69 through 72
      removed outlier: 3.781A  pdb=" N   ALA B 307 " --> pdb=" O   LYS B  72 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   VAL B 107 " --> pdb=" O   CYS B 132 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   CYS B 132 " --> pdb=" O   VAL B 107 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   ILE B 129 " --> pdb=" O   TRP B 267 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   CYS B 269 " --> pdb=" O   ILE B 129 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   GLY B 131 " --> pdb=" O   CYS B 269 " (cutoff:3.500A)
      removed outlier: 7.462A  pdb=" N   ARG B 249 " --> pdb=" O   LEU B 207 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   LEU B 209 " --> pdb=" O   ARG B 249 " (cutoff:3.500A)

    286 hydrogen bonds defined for protein.
    816 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: 2.95

  Time building geometry restraints manager: 1.80 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: 2032
        1.34 -     1.46: 1468
        1.46 -     1.58: 2896
        1.58 -     1.70: 6
        1.70 -     1.82: 68
  Bond restraints: 6470
  Sorted by residual:
  bond pdb=" CB  PHE B 334 "
       pdb=" CG  PHE B 334 "
    ideal  model  delta    sigma   weight residual
    1.502  1.462  0.040 2.30e-02 1.89e+03 3.03e+00
  bond pdb=" CB  PHE A 334 "
       pdb=" CG  PHE A 334 "
    ideal  model  delta    sigma   weight residual
    1.502  1.462  0.040 2.30e-02 1.89e+03 2.98e+00
  bond pdb=" CB  TRP A 267 "
       pdb=" CG  TRP A 267 "
    ideal  model  delta    sigma   weight residual
    1.498  1.445  0.053 3.10e-02 1.04e+03 2.96e+00
  bond pdb=" CB  TRP B 267 "
       pdb=" CG  TRP B 267 "
    ideal  model  delta    sigma   weight residual
    1.498  1.445  0.053 3.10e-02 1.04e+03 2.91e+00
  bond pdb=" CE3 TRP A 267 "
       pdb=" CZ3 TRP A 267 "
    ideal  model  delta    sigma   weight residual
    1.382  1.334  0.048 3.00e-02 1.11e+03 2.54e+00
  ... (remaining 6465 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 8257
        1.84 -     3.69: 414
        3.69 -     5.53: 49
        5.53 -     7.38: 14
        7.38 -     9.22: 2
  Bond angle restraints: 8736
  Sorted by residual:
  angle pdb=" N   ARG A 314 "
        pdb=" CA  ARG A 314 "
        pdb=" C   ARG A 314 "
      ideal   model   delta    sigma   weight residual
     110.53  104.79    5.74 1.32e+00 5.74e-01 1.89e+01
  angle pdb=" N   ARG B 314 "
        pdb=" CA  ARG B 314 "
        pdb=" C   ARG B 314 "
      ideal   model   delta    sigma   weight residual
     110.53  104.81    5.72 1.32e+00 5.74e-01 1.87e+01
  angle pdb=" N   VAL B 296 "
        pdb=" CA  VAL B 296 "
        pdb=" C   VAL B 296 "
      ideal   model   delta    sigma   weight residual
     108.86  114.58   -5.72 1.63e+00 3.76e-01 1.23e+01
  angle pdb=" N   VAL A 296 "
        pdb=" CA  VAL A 296 "
        pdb=" C   VAL A 296 "
      ideal   model   delta    sigma   weight residual
     108.86  114.54   -5.68 1.63e+00 3.76e-01 1.21e+01
  angle pdb=" CA  THR B 313 "
        pdb=" C   THR B 313 "
        pdb=" N   ARG B 314 "
      ideal   model   delta    sigma   weight residual
     117.30  113.64    3.66 1.16e+00 7.43e-01 9.97e+00
  ... (remaining 8731 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.77: 3750
       24.77 -    49.55: 70
       49.55 -    74.32: 14
       74.32 -    99.09: 6
       99.09 -   123.87: 2
  Dihedral angle restraints: 3842
    sinusoidal: 1564
      harmonic: 2278
  Sorted by residual:
  dihedral pdb=" CD  ARG A 314 "
           pdb=" NE  ARG A 314 "
           pdb=" CZ  ARG A 314 "
           pdb=" NH1 ARG A 314 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -62.90   62.90     1      1.00e+01 1.00e-02 5.23e+01
  dihedral pdb=" CD  ARG B 314 "
           pdb=" NE  ARG B 314 "
           pdb=" CZ  ARG B 314 "
           pdb=" NH1 ARG B 314 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -62.88   62.88     1      1.00e+01 1.00e-02 5.22e+01
  dihedral pdb=" CA  GLN A 242 "
           pdb=" C   GLN A 242 "
           pdb=" N   LYS A 243 "
           pdb=" CA  LYS A 243 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.14   23.86     0      5.00e+00 4.00e-02 2.28e+01
  ... (remaining 3839 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 634
       0.053 -    0.105: 263
       0.105 -    0.158: 49
       0.158 -    0.211: 6
       0.211 -    0.263: 2
  Chirality restraints: 954
  Sorted by residual:
  chirality pdb=" CB  ILE A 244 "
            pdb=" CA  ILE A 244 "
            pdb=" CG1 ILE A 244 "
            pdb=" CG2 ILE A 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CB  ILE B 244 "
            pdb=" CA  ILE B 244 "
            pdb=" CG1 ILE B 244 "
            pdb=" CG2 ILE B 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.72e+00
  chirality pdb=" CB  ILE A   5 "
            pdb=" CA  ILE A   5 "
            pdb=" CG1 ILE A   5 "
            pdb=" CG2 ILE A   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.81   -0.17 2.00e-01 2.50e+01 6.98e-01
  ... (remaining 951 not shown)

  Planarity restraints: 1104
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 314 "    0.979 9.50e-02 1.11e+02   4.39e-01 1.17e+02
        pdb=" NE  ARG A 314 "   -0.059 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 314 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 314 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 314 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 314 "    0.979 9.50e-02 1.11e+02   4.39e-01 1.16e+02
        pdb=" NE  ARG B 314 "   -0.059 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 314 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 314 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 314 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 227 "   -0.017 2.00e-02 2.50e+03   2.36e-02 9.73e+00
        pdb=" CG  PHE B 227 "    0.051 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 227 "   -0.027 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 227 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 227 "    0.013 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 227 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 227 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1101 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 269
        2.69 -     3.24: 7059
        3.24 -     3.80: 10501
        3.80 -     4.35: 14213
        4.35 -     4.90: 22358
  Nonbonded interactions: 54400
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 148 "
            pdb=" OH  TYR B 156 "
     model   vdw
     2.138 3.040
  nonbonded pdb=" OH  TYR A 156 "
            pdb=" O   GLY B 148 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" OD2 ASP B 347 "
            pdb=" ND2 ASN B 349 "
     model   vdw
     2.174 3.120
  nonbonded pdb=" OD2 ASP A 347 "
            pdb=" ND2 ASN A 349 "
     model   vdw
     2.175 3.120
  nonbonded pdb=" OE2 GLU B  12 "
            pdb=" NE1 TRP B  23 "
     model   vdw
     2.187 3.120
  ... (remaining 54395 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             33.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.000
  Extract box with map and model:          25.040
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     25.080
  Find NCS groups from input model:        0.140
  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:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   87.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6031
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      :  0.015   0.716   6472  Z= 1.315
  Angle     :  0.928   9.219   8736  Z= 0.515
  Chirality :  0.056   0.263    954
  Planarity :  0.020   0.439   1104
  Dihedral  : 12.219 123.867   2378
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 33.42
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  6.91 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  2.42 %
    Favored  : 97.28 %
  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: -4.07 (0.25), residues: 782
  helix: -3.57 (0.22), residues: 242
  sheet: -2.83 (0.29), residues: 174
  loop : -1.80 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.004   TRP A 267 
 HIS   0.008   0.002   HIS B 133 
 PHE   0.051   0.004   PHE B 227 
 TYR   0.036   0.004   TYR A 156 
 ARG   0.009   0.001   ARG A  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.31097 (  286)
  hydrogen bonds       : angle      10.46486 (  816)
  covalent geometry    : bond        0.00859 ( 6470)
  covalent geometry    : angle       0.92779 ( 8736)
  Misc. bond           : bond        0.71547 (    2)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 184
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 186
  average time/residue: 0.3579
  time to fit residues: 79.6180
Evaluate side-chains
  91 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 89
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain B residue  314 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    9.9990
   chunk 59 optimal weight:    8.9990
   chunk 32 optimal weight:    5.9990
   chunk 20 optimal weight:   10.0000
   chunk 39 optimal weight:   20.0000
   chunk 31 optimal weight:   10.0000
   chunk 61 optimal weight:    7.9990
   chunk 23 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 45 optimal weight:    8.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  96 ASN
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 198 GLN
A 228 GLN
A 349 ASN
A 385 ASN
B  96 ASN
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 198 GLN
B 349 ASN
B 385 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.056695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.043606 restraints weight = 35340.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.045081 restraints weight = 24526.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.046242 restraints weight = 18550.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.4370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6472  Z= 0.200
  Angle     :  0.758   7.336   8736  Z= 0.403
  Chirality :  0.047   0.154    954
  Planarity :  0.005   0.045   1104
  Dihedral  :  9.863 120.209    868
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 23.03
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.07 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 12.08 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.38 (0.26), residues: 782
  helix: -1.18 (0.26), residues: 326
  sheet: -1.95 (0.34), residues: 162
  loop : -1.55 (0.32), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP B 124 
 HIS   0.009   0.002   HIS B  40 
 PHE   0.021   0.002   PHE A 197 
 TYR   0.013   0.001   TYR B 235 
 ARG   0.008   0.001   ARG B 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05233 (  286)
  hydrogen bonds       : angle       6.26885 (  816)
  covalent geometry    : bond        0.00413 ( 6470)
  covalent geometry    : angle       0.75820 ( 8736)
  Misc. bond           : bond        0.00091 (    2)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.567 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9311 (mm)
REVERT: A  180 MET cc_start: 0.8226 (ppp) cc_final: 0.6184 (tmm)
REVERT: A  182 MET cc_start: 0.8163 (tpp) cc_final: 0.7962 (mtp)
REVERT: A  223 PHE cc_start: 0.9105 (m-80) cc_final: 0.8716 (m-80)
REVERT: A  227 PHE cc_start: 0.9550 (m-80) cc_final: 0.9250 (m-10)
REVERT: A  254 MET cc_start: 0.9033 (tpp) cc_final: 0.8708 (tpp)
REVERT: A  291 MET cc_start: 0.9345 (mpp) cc_final: 0.9117 (mmm)
REVERT: A  309 HIS cc_start: 0.9206 (p90) cc_final: 0.8989 (p90)
REVERT: B   44 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9329 (mm)
REVERT: B   91 MET cc_start: 0.9086 (mmt) cc_final: 0.8832 (mmm)
REVERT: B  153 GLU cc_start: 0.8615 (pt0) cc_final: 0.8353 (pm20)
REVERT: B  223 PHE cc_start: 0.9108 (m-80) cc_final: 0.8731 (m-80)
REVERT: B  227 PHE cc_start: 0.9529 (m-80) cc_final: 0.9276 (m-80)
REVERT: B  254 MET cc_start: 0.9065 (tpp) cc_final: 0.8740 (tpp)
REVERT: B  309 HIS cc_start: 0.9211 (p90) cc_final: 0.9001 (p90)
  outliers start: 20
  outliers final: 8
  residues processed: 119
  average time/residue: 0.2199
  time to fit residues: 34.0451
Evaluate side-chains
  90 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  232 ASP
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  232 ASP
Chi-restraints excluded: chain B residue  314 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 60 optimal weight:    9.9990
   chunk 1 optimal weight:   40.0000
   chunk 4 optimal weight:    8.9990
   chunk 67 optimal weight:   30.0000
   chunk 31 optimal weight:    7.9990
   chunk 0 optimal weight:   30.0000
   chunk 44 optimal weight:    7.9990
   chunk 77 optimal weight:    5.9990
   chunk 76 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 57 optimal weight:    6.9990
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.055360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.042148 restraints weight = 35937.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.043531 restraints weight = 24982.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.044648 restraints weight = 19089.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.5229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6472  Z= 0.186
  Angle     :  0.670   5.480   8736  Z= 0.353
  Chirality :  0.043   0.139    954
  Planarity :  0.004   0.035   1104
  Dihedral  :  9.594 118.552    868
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 22.07
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.96 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 15.56 %
    Favored  : 82.18 %
  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: -1.16 (0.29), residues: 782
  helix: -0.03 (0.29), residues: 318
  sheet: -1.34 (0.38), residues: 148
  loop : -1.08 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 124 
 HIS   0.006   0.001   HIS B  40 
 PHE   0.018   0.002   PHE B 197 
 TYR   0.007   0.001   TYR B 235 
 ARG   0.004   0.001   ARG A 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04007 (  286)
  hydrogen bonds       : angle       5.76651 (  816)
  covalent geometry    : bond        0.00399 ( 6470)
  covalent geometry    : angle       0.66994 ( 8736)
  Misc. bond           : bond        0.00008 (    2)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 1.767 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9280 (mm)
REVERT: A  180 MET cc_start: 0.8334 (ppp) cc_final: 0.6595 (tmm)
REVERT: A  223 PHE cc_start: 0.9127 (m-80) cc_final: 0.8720 (m-80)
REVERT: A  254 MET cc_start: 0.8985 (tpp) cc_final: 0.8753 (tpp)
REVERT: A  291 MET cc_start: 0.9394 (mpp) cc_final: 0.9193 (mmm)
REVERT: A  360 GLU cc_start: 0.9505 (mt-10) cc_final: 0.9084 (mp0)
REVERT: A  372 MET cc_start: 0.8565 (ptp) cc_final: 0.7262 (mtt)
REVERT: B   18 MET cc_start: 0.9297 (mmm) cc_final: 0.9079 (mmm)
REVERT: B   44 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9287 (mm)
REVERT: B  182 MET cc_start: 0.8260 (tpt) cc_final: 0.7662 (ttm)
REVERT: B  223 PHE cc_start: 0.9111 (m-80) cc_final: 0.8702 (m-80)
REVERT: B  254 MET cc_start: 0.8968 (tpp) cc_final: 0.8739 (tpp)
REVERT: B  291 MET cc_start: 0.9430 (mmm) cc_final: 0.9087 (mmm)
REVERT: B  360 GLU cc_start: 0.9535 (mt-10) cc_final: 0.9118 (mp0)
REVERT: B  372 MET cc_start: 0.8568 (ptp) cc_final: 0.7335 (mtt)
  outliers start: 15
  outliers final: 12
  residues processed: 97
  average time/residue: 0.3804
  time to fit residues: 47.5714
Evaluate side-chains
  89 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  232 ASP
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain A residue  321 LYS
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  232 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  321 LYS
Chi-restraints excluded: chain B residue  398 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 51 optimal weight:    9.9990
   chunk 49 optimal weight:    7.9990
   chunk 50 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 71 optimal weight:    6.9990
   chunk 34 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 27 optimal weight:   20.0000
   chunk 24 optimal weight:    4.9990
   chunk 69 optimal weight:    8.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.054262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.041296 restraints weight = 36004.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.042719 restraints weight = 24552.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.043773 restraints weight = 18528.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8682
moved from start:          0.5777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6472  Z= 0.162
  Angle     :  0.610   6.094   8736  Z= 0.322
  Chirality :  0.043   0.126    954
  Planarity :  0.003   0.028   1104
  Dihedral  :  9.362 117.932    868
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 21.20
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.48 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 14.20 %
    Favored  : 81.57 %
  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: -0.87 (0.30), residues: 782
  helix:  0.16 (0.29), residues: 330
  sheet: -1.26 (0.37), residues: 170
  loop : -0.79 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 267 
 HIS   0.006   0.001   HIS A  40 
 PHE   0.012   0.002   PHE B 197 
 TYR   0.017   0.001   TYR A 231 
 ARG   0.003   0.001   ARG A 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03577 (  286)
  hydrogen bonds       : angle       5.60775 (  816)
  covalent geometry    : bond        0.00353 ( 6470)
  covalent geometry    : angle       0.61010 ( 8736)
  Misc. bond           : bond        0.00007 (    2)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 77
  time to evaluate  : 0.704 
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   18 MET cc_start: 0.9346 (mmm) cc_final: 0.9094 (mmm)
REVERT: A  180 MET cc_start: 0.8615 (ppp) cc_final: 0.8019 (tmm)
REVERT: A  187 LYS cc_start: 0.9648 (OUTLIER) cc_final: 0.9161 (tppt)
REVERT: A  223 PHE cc_start: 0.9127 (m-80) cc_final: 0.8616 (m-80)
REVERT: A  227 PHE cc_start: 0.9426 (m-80) cc_final: 0.9183 (m-80)
REVERT: A  254 MET cc_start: 0.8974 (tpp) cc_final: 0.8627 (tpp)
REVERT: A  267 TRP cc_start: 0.9283 (OUTLIER) cc_final: 0.9013 (t-100)
REVERT: A  291 MET cc_start: 0.9397 (mpp) cc_final: 0.9171 (mmm)
REVERT: B   84 GLU cc_start: 0.9367 (pt0) cc_final: 0.9061 (pp20)
REVERT: B  180 MET cc_start: 0.8495 (ppp) cc_final: 0.7988 (ppp)
REVERT: B  182 MET cc_start: 0.8168 (tpt) cc_final: 0.7948 (tmm)
REVERT: B  223 PHE cc_start: 0.9154 (m-80) cc_final: 0.8696 (m-80)
REVERT: B  254 MET cc_start: 0.8999 (tpp) cc_final: 0.8629 (tpp)
REVERT: B  267 TRP cc_start: 0.9282 (OUTLIER) cc_final: 0.9013 (t-100)
REVERT: B  291 MET cc_start: 0.9413 (mmm) cc_final: 0.9066 (mmm)
  outliers start: 28
  outliers final: 15
  residues processed: 98
  average time/residue: 0.2373
  time to fit residues: 29.5279
Evaluate side-chains
  87 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  187 LYS
Chi-restraints excluded: chain A residue  232 ASP
Chi-restraints excluded: chain A residue  259 MET
Chi-restraints excluded: chain A residue  267 TRP
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain A residue  317 ARG
Chi-restraints excluded: chain A residue  321 LYS
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  232 ASP
Chi-restraints excluded: chain B residue  267 TRP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  321 LYS
Chi-restraints excluded: chain B residue  398 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    8.9990
   chunk 44 optimal weight:    0.2980
   chunk 61 optimal weight:    9.9990
   chunk 60 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 12 optimal weight:   20.0000
   chunk 71 optimal weight:   20.0000
   chunk 41 optimal weight:    2.9990
   chunk 32 optimal weight:   20.0000
   chunk 30 optimal weight:   10.0000
   overall best weight:    3.6588

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

Flipped N/Q/H residues before XYZ refinement:
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.054185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.041621 restraints weight = 34920.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.043034 restraints weight = 23613.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.044112 restraints weight = 17735.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.6267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6472  Z= 0.137
  Angle     :  0.637   5.571   8736  Z= 0.333
  Chirality :  0.043   0.136    954
  Planarity :  0.003   0.025   1104
  Dihedral  :  9.238 116.736    868
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 17.63
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.45 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 14.80 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.30), residues: 782
  helix:  0.31 (0.29), residues: 336
  sheet: -1.12 (0.38), residues: 146
  loop : -1.07 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 267 
 HIS   0.007   0.001   HIS A 342 
 PHE   0.010   0.001   PHE B 334 
 TYR   0.015   0.001   TYR A 231 
 ARG   0.003   0.001   ARG A 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03360 (  286)
  hydrogen bonds       : angle       5.62796 (  816)
  covalent geometry    : bond        0.00305 ( 6470)
  covalent geometry    : angle       0.63679 ( 8736)
  Misc. bond           : bond        0.00012 (    2)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.765 
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   13 MET cc_start: 0.9164 (mmp) cc_final: 0.8752 (mpp)
REVERT: A   84 GLU cc_start: 0.9381 (pt0) cc_final: 0.9098 (pp20)
REVERT: A  180 MET cc_start: 0.8582 (ppp) cc_final: 0.7983 (tmm)
REVERT: A  223 PHE cc_start: 0.9112 (m-80) cc_final: 0.8572 (m-80)
REVERT: A  291 MET cc_start: 0.9377 (mpp) cc_final: 0.9140 (mmm)
REVERT: A  318 MET cc_start: 0.7156 (pmm) cc_final: 0.6929 (pmm)
REVERT: B   13 MET cc_start: 0.9168 (mmp) cc_final: 0.8751 (mpp)
REVERT: B   84 GLU cc_start: 0.9357 (pt0) cc_final: 0.9049 (pp20)
REVERT: B  180 MET cc_start: 0.8547 (ppp) cc_final: 0.8086 (ppp)
REVERT: B  182 MET cc_start: 0.8093 (tpt) cc_final: 0.7882 (tmm)
REVERT: B  223 PHE cc_start: 0.9125 (m-80) cc_final: 0.8547 (m-80)
REVERT: B  227 PHE cc_start: 0.9478 (m-80) cc_final: 0.9268 (m-80)
REVERT: B  290 MET cc_start: 0.8891 (ptp) cc_final: 0.8406 (ptp)
REVERT: B  291 MET cc_start: 0.9438 (mmm) cc_final: 0.8920 (mmm)
  outliers start: 21
  outliers final: 12
  residues processed: 94
  average time/residue: 0.2195
  time to fit residues: 26.6535
Evaluate side-chains
  80 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  232 ASP
Chi-restraints excluded: chain A residue  259 MET
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  232 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  321 LYS
Chi-restraints excluded: chain B residue  398 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 0 optimal weight:   40.0000
   chunk 39 optimal weight:   40.0000
   chunk 53 optimal weight:    9.9990
   chunk 42 optimal weight:   10.0000
   chunk 27 optimal weight:   50.0000
   chunk 48 optimal weight:    6.9990
   chunk 35 optimal weight:   50.0000
   chunk 68 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   chunk 72 optimal weight:    4.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.052497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.040135 restraints weight = 35453.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.041537 restraints weight = 24115.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.042574 restraints weight = 18127.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8721
moved from start:          0.6539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6472  Z= 0.174
  Angle     :  0.667   9.714   8736  Z= 0.348
  Chirality :  0.044   0.197    954
  Planarity :  0.004   0.040   1104
  Dihedral  :  9.273 117.859    868
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 21.04
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.35 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 15.71 %
    Favored  : 81.42 %
  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: -0.52 (0.30), residues: 782
  helix:  0.45 (0.29), residues: 334
  sheet: -0.97 (0.37), residues: 164
  loop : -0.71 (0.40), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 267 
 HIS   0.005   0.001   HIS A 342 
 PHE   0.012   0.002   PHE B 334 
 TYR   0.014   0.001   TYR A 231 
 ARG   0.006   0.001   ARG A 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03464 (  286)
  hydrogen bonds       : angle       5.60984 (  816)
  covalent geometry    : bond        0.00379 ( 6470)
  covalent geometry    : angle       0.66723 ( 8736)
  Misc. bond           : bond        0.00016 (    2)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.685 
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   13 MET cc_start: 0.9182 (mmt) cc_final: 0.8800 (mpp)
REVERT: A   84 GLU cc_start: 0.9365 (pt0) cc_final: 0.9086 (pp20)
REVERT: A   91 MET cc_start: 0.8956 (tpp) cc_final: 0.8712 (tpp)
REVERT: A  180 MET cc_start: 0.8621 (ppp) cc_final: 0.8040 (tmm)
REVERT: A  223 PHE cc_start: 0.9169 (m-80) cc_final: 0.8616 (m-80)
REVERT: A  254 MET cc_start: 0.8869 (tpp) cc_final: 0.8630 (tpp)
REVERT: A  267 TRP cc_start: 0.9295 (OUTLIER) cc_final: 0.8904 (t-100)
REVERT: A  291 MET cc_start: 0.9380 (mpp) cc_final: 0.9088 (mmm)
REVERT: B   13 MET cc_start: 0.9181 (mmt) cc_final: 0.8807 (mpp)
REVERT: B   84 GLU cc_start: 0.9339 (pt0) cc_final: 0.9042 (pp20)
REVERT: B  180 MET cc_start: 0.8486 (ppp) cc_final: 0.8017 (ppp)
REVERT: B  223 PHE cc_start: 0.9172 (m-80) cc_final: 0.8642 (m-80)
REVERT: B  290 MET cc_start: 0.8769 (ptp) cc_final: 0.8146 (ptp)
REVERT: B  291 MET cc_start: 0.9450 (mmm) cc_final: 0.8982 (mmm)
  outliers start: 19
  outliers final: 13
  residues processed: 77
  average time/residue: 0.1913
  time to fit residues: 20.1059
Evaluate side-chains
  75 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  232 ASP
Chi-restraints excluded: chain A residue  259 MET
Chi-restraints excluded: chain A residue  267 TRP
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  232 ASP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  321 LYS
Chi-restraints excluded: chain B residue  398 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 66 optimal weight:   50.0000
   chunk 69 optimal weight:    0.1980
   chunk 54 optimal weight:   10.0000
   chunk 58 optimal weight:    9.9990
   chunk 65 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 53 optimal weight:   20.0000
   chunk 59 optimal weight:   10.0000
   overall best weight:    2.8388

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.054476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.041786 restraints weight = 34577.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.043226 restraints weight = 23700.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.044316 restraints weight = 17827.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8685
moved from start:          0.6892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6472  Z= 0.123
  Angle     :  0.650   8.438   8736  Z= 0.336
  Chirality :  0.044   0.144    954
  Planarity :  0.003   0.025   1104
  Dihedral  :  9.066 114.302    868
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 16.91
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.45 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.31 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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 (0.30), residues: 782
  helix:  0.55 (0.29), residues: 334
  sheet: -0.70 (0.38), residues: 150
  loop : -0.83 (0.37), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 267 
 HIS   0.003   0.001   HIS B 309 
 PHE   0.009   0.001   PHE B 197 
 TYR   0.011   0.001   TYR A 231 
 ARG   0.006   0.001   ARG B 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03210 (  286)
  hydrogen bonds       : angle       5.43138 (  816)
  covalent geometry    : bond        0.00276 ( 6470)
  covalent geometry    : angle       0.65003 ( 8736)
  Misc. bond           : bond        0.00024 (    2)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.681 
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: symmetry clash
REVERT: A   84 GLU cc_start: 0.9368 (pt0) cc_final: 0.9098 (pp20)
REVERT: A   91 MET cc_start: 0.8987 (tpp) cc_final: 0.8694 (tpp)
REVERT: A  180 MET cc_start: 0.8541 (ppp) cc_final: 0.8006 (tmm)
REVERT: A  223 PHE cc_start: 0.9100 (m-80) cc_final: 0.8436 (m-80)
REVERT: A  291 MET cc_start: 0.9352 (mpp) cc_final: 0.8979 (mmm)
REVERT: A  334 PHE cc_start: 0.9688 (m-80) cc_final: 0.9268 (m-80)
REVERT: B   13 MET cc_start: 0.9140 (mmt) cc_final: 0.8829 (mpp)
REVERT: B   18 MET cc_start: 0.9680 (mmm) cc_final: 0.9474 (mpp)
REVERT: B  180 MET cc_start: 0.8533 (ppp) cc_final: 0.8056 (ppp)
REVERT: B  223 PHE cc_start: 0.9142 (m-80) cc_final: 0.8557 (m-80)
REVERT: B  254 MET cc_start: 0.8768 (tpp) cc_final: 0.8280 (mpp)
REVERT: B  267 TRP cc_start: 0.9297 (OUTLIER) cc_final: 0.8820 (t-100)
REVERT: B  290 MET cc_start: 0.8824 (ptp) cc_final: 0.8228 (ptp)
REVERT: B  291 MET cc_start: 0.9426 (mmm) cc_final: 0.8950 (mmm)
  outliers start: 16
  outliers final: 11
  residues processed: 81
  average time/residue: 0.1582
  time to fit residues: 17.8343
Evaluate side-chains
  73 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  232 ASP
Chi-restraints excluded: chain A residue  259 MET
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  232 ASP
Chi-restraints excluded: chain B residue  267 TRP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  398 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 20 optimal weight:   30.0000
   chunk 16 optimal weight:    7.9990
   chunk 18 optimal weight:   20.0000
   chunk 49 optimal weight:   40.0000
   chunk 73 optimal weight:   30.0000
   chunk 34 optimal weight:    8.9990
   chunk 46 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 27 optimal weight:   50.0000
   chunk 7 optimal weight:    8.9990
   overall best weight:    8.3992

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

Flipped N/Q/H residues before XYZ refinement:
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.051214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.039039 restraints weight = 36892.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.040412 restraints weight = 25174.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.041449 restraints weight = 18938.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8754
moved from start:          0.7018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6472  Z= 0.201
  Angle     :  0.670   9.386   8736  Z= 0.353
  Chirality :  0.043   0.131    954
  Planarity :  0.004   0.032   1104
  Dihedral  :  8.972 113.410    868
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 23.19
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.22 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.77 %
    Favored  : 80.51 %
  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: -0.48 (0.30), residues: 782
  helix:  0.52 (0.29), residues: 336
  sheet: -0.95 (0.36), residues: 164
  loop : -0.75 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 267 
 HIS   0.004   0.002   HIS A 248 
 PHE   0.013   0.002   PHE A 227 
 TYR   0.014   0.001   TYR A 231 
 ARG   0.006   0.001   ARG B 317 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03670 (  286)
  hydrogen bonds       : angle       5.53110 (  816)
  covalent geometry    : bond        0.00427 ( 6470)
  covalent geometry    : angle       0.66957 ( 8736)
  Misc. bond           : bond        0.00018 (    2)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.679 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 GLU cc_start: 0.9366 (pt0) cc_final: 0.9130 (pp20)
REVERT: A  180 MET cc_start: 0.8526 (ppp) cc_final: 0.8019 (tmm)
REVERT: A  223 PHE cc_start: 0.9193 (m-80) cc_final: 0.8558 (m-80)
REVERT: A  254 MET cc_start: 0.8887 (tpp) cc_final: 0.8586 (mpp)
REVERT: A  267 TRP cc_start: 0.9279 (OUTLIER) cc_final: 0.8909 (t-100)
REVERT: A  291 MET cc_start: 0.9363 (mpp) cc_final: 0.9054 (mmm)
REVERT: A  334 PHE cc_start: 0.9687 (m-80) cc_final: 0.9252 (m-80)
REVERT: B   13 MET cc_start: 0.9189 (mmt) cc_final: 0.8789 (mpp)
REVERT: B  180 MET cc_start: 0.8447 (ppp) cc_final: 0.8080 (ppp)
REVERT: B  223 PHE cc_start: 0.9231 (m-80) cc_final: 0.8624 (m-80)
REVERT: B  267 TRP cc_start: 0.9270 (OUTLIER) cc_final: 0.8895 (t-100)
REVERT: B  290 MET cc_start: 0.8802 (ptp) cc_final: 0.8452 (ptp)
REVERT: B  291 MET cc_start: 0.9428 (mmm) cc_final: 0.9137 (mmm)
  outliers start: 18
  outliers final: 12
  residues processed: 75
  average time/residue: 0.1632
  time to fit residues: 17.0554
Evaluate side-chains
  73 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  232 ASP
Chi-restraints excluded: chain A residue  259 MET
Chi-restraints excluded: chain A residue  267 TRP
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  232 ASP
Chi-restraints excluded: chain B residue  267 TRP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  398 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 18 optimal weight:    6.9990
   chunk 28 optimal weight:   20.0000
   chunk 34 optimal weight:    7.9990
   chunk 24 optimal weight:    0.0870
   chunk 59 optimal weight:    6.9990
   chunk 74 optimal weight:    7.9990
   chunk 17 optimal weight:    9.9990
   chunk 19 optimal weight:    8.9990
   chunk 39 optimal weight:   40.0000
   chunk 75 optimal weight:    0.0470
   chunk 69 optimal weight:    7.9990
   overall best weight:    4.4262

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

Flipped N/Q/H residues before XYZ refinement:
** B 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.052833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.040397 restraints weight = 36361.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.041807 restraints weight = 24694.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.042871 restraints weight = 18597.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8722
moved from start:          0.7237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6472  Z= 0.143
  Angle     :  0.689   9.488   8736  Z= 0.355
  Chirality :  0.043   0.133    954
  Planarity :  0.003   0.024   1104
  Dihedral  :  8.792 110.366    868
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 18.18
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.84 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.82 %
    Favored  : 79.76 %
  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: -0.48 (0.30), residues: 782
  helix:  0.50 (0.29), residues: 336
  sheet: -0.75 (0.40), residues: 122
  loop : -0.90 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 267 
 HIS   0.003   0.001   HIS A  67 
 PHE   0.010   0.001   PHE A 227 
 TYR   0.011   0.001   TYR A 231 
 ARG   0.005   0.001   ARG B 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03461 (  286)
  hydrogen bonds       : angle       5.47160 (  816)
  covalent geometry    : bond        0.00312 ( 6470)
  covalent geometry    : angle       0.68891 ( 8736)
  Misc. bond           : bond        0.00013 (    2)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.702 
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: symmetry clash
REVERT: A   84 GLU cc_start: 0.9372 (pt0) cc_final: 0.9129 (pp20)
REVERT: A   91 MET cc_start: 0.8918 (tpp) cc_final: 0.8603 (tpp)
REVERT: A  180 MET cc_start: 0.8476 (ppp) cc_final: 0.7986 (tmm)
REVERT: A  223 PHE cc_start: 0.9151 (m-80) cc_final: 0.8837 (m-80)
REVERT: A  254 MET cc_start: 0.8862 (tpp) cc_final: 0.8411 (mpp)
REVERT: A  267 TRP cc_start: 0.9271 (OUTLIER) cc_final: 0.8787 (t-100)
REVERT: A  290 MET cc_start: 0.8974 (mmp) cc_final: 0.8569 (mtt)
REVERT: A  291 MET cc_start: 0.9364 (mpp) cc_final: 0.8866 (mmm)
REVERT: B   13 MET cc_start: 0.9172 (mmt) cc_final: 0.8793 (mpp)
REVERT: B  180 MET cc_start: 0.8408 (ppp) cc_final: 0.8041 (ppp)
REVERT: B  223 PHE cc_start: 0.9219 (m-80) cc_final: 0.8565 (m-80)
REVERT: B  254 MET cc_start: 0.8858 (tpp) cc_final: 0.8465 (mpp)
REVERT: B  267 TRP cc_start: 0.9277 (OUTLIER) cc_final: 0.8842 (t-100)
REVERT: B  290 MET cc_start: 0.8846 (ptp) cc_final: 0.8506 (ptp)
REVERT: B  291 MET cc_start: 0.9409 (mmm) cc_final: 0.9110 (mmm)
  outliers start: 16
  outliers final: 11
  residues processed: 71
  average time/residue: 0.1684
  time to fit residues: 16.6695
Evaluate side-chains
  71 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  232 ASP
Chi-restraints excluded: chain A residue  267 TRP
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  232 ASP
Chi-restraints excluded: chain B residue  267 TRP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  398 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 38 optimal weight:   10.0000
   chunk 21 optimal weight:    9.9990
   chunk 74 optimal weight:    9.9990
   chunk 34 optimal weight:    9.9990
   chunk 60 optimal weight:   10.0000
   chunk 51 optimal weight:   10.0000
   chunk 13 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 36 optimal weight:    5.9990
   chunk 76 optimal weight:   20.0000
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 185 GLN
** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 170 HIS
** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.051294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.039091 restraints weight = 37033.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.040483 restraints weight = 25351.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.041527 restraints weight = 19056.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8741
moved from start:          0.7334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6472  Z= 0.176
  Angle     :  0.705   9.994   8736  Z= 0.366
  Chirality :  0.043   0.127    954
  Planarity :  0.004   0.025   1104
  Dihedral  :  8.683 105.669    868
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 22.31
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.96 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 18.43 %
    Favored  : 79.61 %
  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: -0.45 (0.30), residues: 782
  helix:  0.46 (0.29), residues: 334
  sheet: -0.71 (0.41), residues: 122
  loop : -0.81 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 267 
 HIS   0.004   0.001   HIS A  67 
 PHE   0.012   0.002   PHE A 227 
 TYR   0.011   0.001   TYR A 231 
 ARG   0.006   0.001   ARG B 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03587 (  286)
  hydrogen bonds       : angle       5.52381 (  816)
  covalent geometry    : bond        0.00377 ( 6470)
  covalent geometry    : angle       0.70490 ( 8736)
  Misc. bond           : bond        0.00005 (    2)

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

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

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1564 Ramachandran restraints generated.
    782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.804 
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: symmetry clash
REVERT: A   84 GLU cc_start: 0.9395 (pt0) cc_final: 0.9163 (pp20)
REVERT: A   91 MET cc_start: 0.8965 (tpp) cc_final: 0.8634 (tpp)
REVERT: A  180 MET cc_start: 0.8462 (ppp) cc_final: 0.7981 (tmm)
REVERT: A  223 PHE cc_start: 0.9201 (m-80) cc_final: 0.8882 (m-80)
REVERT: A  254 MET cc_start: 0.8932 (tpp) cc_final: 0.8493 (mpp)
REVERT: A  267 TRP cc_start: 0.9253 (OUTLIER) cc_final: 0.8764 (t-100)
REVERT: A  290 MET cc_start: 0.9013 (mmp) cc_final: 0.8561 (mtt)
REVERT: A  291 MET cc_start: 0.9361 (mpp) cc_final: 0.8873 (mmm)
REVERT: B   13 MET cc_start: 0.9213 (mmt) cc_final: 0.8790 (mpp)
REVERT: B  180 MET cc_start: 0.8376 (ppp) cc_final: 0.7993 (ppp)
REVERT: B  223 PHE cc_start: 0.9260 (m-80) cc_final: 0.8604 (m-80)
REVERT: B  254 MET cc_start: 0.8957 (tpp) cc_final: 0.8604 (mpp)
REVERT: B  267 TRP cc_start: 0.9271 (OUTLIER) cc_final: 0.8840 (t-100)
REVERT: B  290 MET cc_start: 0.8847 (ptp) cc_final: 0.8529 (ptp)
REVERT: B  291 MET cc_start: 0.9371 (mmm) cc_final: 0.9086 (mmm)
  outliers start: 13
  outliers final: 11
  residues processed: 68
  average time/residue: 0.1781
  time to fit residues: 16.9249
Evaluate side-chains
  71 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  232 ASP
Chi-restraints excluded: chain A residue  267 TRP
Chi-restraints excluded: chain A residue  314 ARG
Chi-restraints excluded: chain B residue  107 VAL
Chi-restraints excluded: chain B residue  130 ILE
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  232 ASP
Chi-restraints excluded: chain B residue  267 TRP
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  398 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:   20.0000
   chunk 53 optimal weight:    0.0970
   chunk 15 optimal weight:    9.9990
   chunk 65 optimal weight:   30.0000
   chunk 27 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 42 optimal weight:    0.0050
   chunk 67 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   chunk 61 optimal weight:    8.9990
   chunk 49 optimal weight:   20.0000
   overall best weight:    3.8198

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

Flipped N/Q/H residues before XYZ refinement:
** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.053343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.041208 restraints weight = 37844.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.042645 restraints weight = 25166.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.043743 restraints weight = 18602.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.7537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6472  Z= 0.136
  Angle     :  0.689  10.136   8736  Z= 0.354
  Chirality :  0.043   0.126    954
  Planarity :  0.003   0.024   1104
  Dihedral  :  8.533 103.442    868
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 17.87
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.09 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 19.03 %
    Favored  : 79.31 %
  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: -0.34 (0.30), residues: 782
  helix:  0.68 (0.29), residues: 326
  sheet: -0.44 (0.42), residues: 122
  loop : -0.98 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 267 
 HIS   0.003   0.001   HIS A  67 
 PHE   0.009   0.001   PHE A 227 
 TYR   0.014   0.001   TYR B 316 
 ARG   0.005   0.000   ARG B 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03358 (  286)
  hydrogen bonds       : angle       5.32002 (  816)
  covalent geometry    : bond        0.00297 ( 6470)
  covalent geometry    : angle       0.68942 ( 8736)
  Misc. bond           : bond        0.00015 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3302.45 seconds
wall clock time: 60 minutes 45.33 seconds (3645.33 seconds total)