Starting phenix.real_space_refine
on Fri Mar 14 00:34:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sq0_25373/03_2025/7sq0_25373.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sq0_25373/03_2025/7sq0_25373.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sq0_25373/03_2025/7sq0_25373.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sq0_25373/03_2025/7sq0_25373.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sq0_25373/03_2025/7sq0_25373.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sq0_25373/03_2025/7sq0_25373.cif"
  }
  resolution = 3.7
  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=   0.001
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 54 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: 8
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P       4      5.49       5
     Mg      2      5.21       5
     S      32      5.16       5
     C    3089      2.51       5
     N     814      2.21       5
     O     932      1.98       5
     H    4286      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9160
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 1421
          Classifications: {'peptide': 94}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 88}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 3059
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 3059
          Classifications: {'peptide': 212}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 9, 'TRANS': 202}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'UNK:plan-1': 19, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "B"
      Number of atoms: 1429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 1429
          Classifications: {'peptide': 94}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 88}
    Chain: "B"
      Number of atoms: 3056
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 3056
          Classifications: {'peptide': 208}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 9, 'TRANS': 198}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'UNK:plan-1': 18}
          Unresolved non-hydrogen planarities: 18
    Chain: "C"
      Number of atoms: 138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 138
          Classifications: {'peptide': 22}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'TRANS': 21}
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 117
          Unresolved non-hydrogen dihedrals: 75
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'PHE:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 40
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   3490  SG  CYS A 287      30.096  41.595  78.100  1.00 78.54           S
  ATOM   3529  SG  CYS A 290      30.245  44.327  76.040  1.00 79.84           S
  ATOM   7977  SG  CYS B 287      27.060  45.006  78.102  1.00 78.23           S
  ATOM   8016  SG  CYS B 290      26.901  42.269  76.059  1.00 79.43           S

  Time building chain proxies: 5.89, per 1000 atoms: 0.64
  Number of scatterers: 9160
  At special positions: 0
  Unit cell: (58.022, 87.466, 91.796, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     Zn      1     29.99
     S      32     16.00
     P       4     15.00
     Mg      2     11.99
     O     932      8.00
     N     814      7.00
     C    3089      6.00
     H    4286      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.26
  Conformation dependent library (CDL) restraints added in 562.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 500 "
        pdb="ZN    ZN A 500 " - pdb=" SG  CYS B 290 "
        pdb="ZN    ZN A 500 " - pdb=" SG  CYS A 290 "
        pdb="ZN    ZN A 500 " - pdb=" SG  CYS A 287 "
        pdb="ZN    ZN A 500 " - pdb=" SG  CYS B 287 "
      Number of angles added : 6


  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1210

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 2 sheets defined
      62.2% alpha, 10.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.77
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 11
      removed outlier: 3.829A  pdb=" N   LEU A   9 " --> pdb=" O   LEU A   5 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ASP A  10 " --> pdb=" O   HIS A   6 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLN A  11 " --> pdb=" O   ASP A   7 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 5 through 11'
    Processing helix  chain 'A' and resid 26 through 42
    Processing helix  chain 'A' and resid 57 through 63
    Processing helix  chain 'A' and resid 86 through 94
      removed outlier: 3.706A  pdb=" N   MET A  90 " --> pdb=" O   ALA A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 116
      removed outlier: 3.614A  pdb=" N   UNK A 105 " --> pdb=" O   UNK A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 135
      removed outlier: 4.093A  pdb=" N   GLY A 135 " --> pdb=" O   PHE A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 155
      removed outlier: 3.806A  pdb=" N   THR A 155 " --> pdb=" O   LYS A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 189
      removed outlier: 3.564A  pdb=" N   LEU A 172 " --> pdb=" O   THR A 168 " (cutoff:3.500A)
      removed outlier: 4.719A  pdb=" N   ARG A 173 " --> pdb=" O   GLY A 169 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.515A  pdb=" N   GLU A 186 " --> pdb=" O   ASN A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 236
      removed outlier: 3.516A  pdb=" N   ASP A 225 " --> pdb=" O   TYR A 221 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   VAL A 226 " --> pdb=" O   PRO A 222 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ARG A 235 " --> pdb=" O   SER A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 267
      removed outlier: 4.362A  pdb=" N   TYR A 254 " --> pdb=" O   PHE A 250 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LEU A 266 " --> pdb=" O   ARG A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 308
      removed outlier: 3.719A  pdb=" N   LYS A 299 " --> pdb=" O   ARG A 295 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   TYR A 300 " --> pdb=" O   MET A 296 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASP A 302 " --> pdb=" O   ASN A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 338
      removed outlier: 3.871A  pdb=" N   ASP A 331 " --> pdb=" O   ALA A 327 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   GLU A 334 " --> pdb=" O   ARG A 330 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   LEU A 336 " --> pdb=" O   TYR A 332 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ILE A 337 " --> pdb=" O   ALA A 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 11
      removed outlier: 3.827A  pdb=" N   LEU B   9 " --> pdb=" O   LEU B   5 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ASP B  10 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   GLN B  11 " --> pdb=" O   ASP B   7 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 5 through 11'
    Processing helix  chain 'B' and resid 26 through 42
    Processing helix  chain 'B' and resid 57 through 63
    Processing helix  chain 'B' and resid 88 through 94
    Processing helix  chain 'B' and resid 98 through 114
      removed outlier: 3.659A  pdb=" N   UNK B 102 " --> pdb=" O   UNK B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 135
      removed outlier: 3.723A  pdb=" N   PHE B 131 " --> pdb=" O   CYS B 127 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ILE B 132 " --> pdb=" O   ALA B 128 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LYS B 133 " --> pdb=" O   SER B 129 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ASP B 134 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 155
      removed outlier: 3.823A  pdb=" N   THR B 155 " --> pdb=" O   LYS B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 189
      removed outlier: 3.537A  pdb=" N   LEU B 172 " --> pdb=" O   THR B 168 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   ARG B 173 " --> pdb=" O   GLY B 169 " (cutoff:3.500A)
      Proline residue:  B 178  - end of helix
      removed outlier: 3.581A  pdb=" N   LYS B 183 " --> pdb=" O   GLU B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 236
      removed outlier: 3.570A  pdb=" N   ARG B 235 " --> pdb=" O   SER B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 267
      removed outlier: 4.369A  pdb=" N   TYR B 254 " --> pdb=" O   PHE B 250 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   LEU B 266 " --> pdb=" O   ARG B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 308
      removed outlier: 3.724A  pdb=" N   LYS B 299 " --> pdb=" O   ARG B 295 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   TYR B 300 " --> pdb=" O   MET B 296 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ASP B 302 " --> pdb=" O   ASN B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 338
      removed outlier: 3.869A  pdb=" N   ASP B 331 " --> pdb=" O   ALA B 327 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLU B 334 " --> pdb=" O   ARG B 330 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   THR B 335 " --> pdb=" O   ASP B 331 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   LEU B 336 " --> pdb=" O   TYR B 332 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ILE B 337 " --> pdb=" O   ALA B 333 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 263 through 281
      removed outlier: 3.562A  pdb=" N   TYR C 280 " --> pdb=" O   ILE C 276 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   TYR C 281 " --> pdb=" O   ILE C 277 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 72
      removed outlier: 6.945A  pdb=" N   LEU A  48 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
      removed outlier: 8.429A  pdb=" N   ASP A 164 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   LEU A  50 " --> pdb=" O   ASP A 164 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   PHE A  19 " --> pdb=" O   PHE A 163 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   PHE A 242 " --> pdb=" O   ALA A 272 " (cutoff:3.500A)
      removed outlier: 8.379A  pdb=" N   VAL A 274 " --> pdb=" O   PHE A 242 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   GLY A 244 " --> pdb=" O   VAL A 274 " (cutoff:3.500A)
      removed outlier: 7.759A  pdb=" N   ASN A 276 " --> pdb=" O   GLY A 244 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   CYS A 246 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)
      removed outlier: 7.712A  pdb=" N   VAL A 278 " --> pdb=" O   CYS A 246 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   PHE A 277 " --> pdb=" O   SER A 316 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 71 through 72
      removed outlier: 6.934A  pdb=" N   LEU B  48 " --> pdb=" O   ILE B 162 " (cutoff:3.500A)
      removed outlier: 8.386A  pdb=" N   ASP B 164 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   LEU B  50 " --> pdb=" O   ASP B 164 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   PHE B  19 " --> pdb=" O   PHE B 163 " (cutoff:3.500A)
      removed outlier: 9.765A  pdb=" N   ALA B 272 " --> pdb=" O   CYS B 240 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   PHE B 242 " --> pdb=" O   ALA B 272 " (cutoff:3.500A)
      removed outlier: 8.382A  pdb=" N   VAL B 274 " --> pdb=" O   PHE B 242 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   GLY B 244 " --> pdb=" O   VAL B 274 " (cutoff:3.500A)
      removed outlier: 7.759A  pdb=" N   ASN B 276 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   CYS B 246 " --> pdb=" O   ASN B 276 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   VAL B 278 " --> pdb=" O   CYS B 246 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   PHE B 277 " --> pdb=" O   SER B 316 " (cutoff:3.500A)

    243 hydrogen bonds defined for protein.
    723 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: 2.99

  Time building geometry restraints manager: 2.79 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 4274
        1.03 -     1.23: 12
        1.23 -     1.42: 2072
        1.42 -     1.61: 2850
        1.61 -     1.81: 50
  Bond restraints: 9258
  Sorted by residual:
  bond pdb=" C4  ADP B 401 "
       pdb=" C5  ADP B 401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.382  0.108 2.00e-02 2.50e+03 2.94e+01
  bond pdb=" C4  ADP A 401 "
       pdb=" C5  ADP A 401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.382  0.108 2.00e-02 2.50e+03 2.93e+01
  bond pdb=" C5  ADP B 401 "
       pdb=" C6  ADP B 401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.407  0.083 2.00e-02 2.50e+03 1.71e+01
  bond pdb=" C5  ADP A 401 "
       pdb=" C6  ADP A 401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.407  0.083 2.00e-02 2.50e+03 1.70e+01
  bond pdb=" C8  ADP B 401 "
       pdb=" N7  ADP B 401 "
    ideal  model  delta    sigma   weight residual
    1.350  1.309  0.041 2.00e-02 2.50e+03 4.17e+00
  ... (remaining 9253 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.88: 16484
        7.88 -    15.76: 10
       15.76 -    23.64: 2
       23.64 -    31.52: 4
       31.52 -    39.40: 9
  Bond angle restraints: 16509
  Sorted by residual:
  angle pdb=" C   PRO A 222 "
        pdb=" CA  PRO A 222 "
        pdb=" HA  PRO A 222 "
      ideal   model   delta    sigma   weight residual
     109.00   69.60   39.40 3.00e+00 1.11e-01 1.73e+02
  angle pdb=" CB  LEU C 272 "
        pdb=" CA  LEU C 272 "
        pdb=" HA  LEU C 272 "
      ideal   model   delta    sigma   weight residual
     109.00   73.92   35.08 3.00e+00 1.11e-01 1.37e+02
  angle pdb=" CB  LYS A 223 "
        pdb=" CA  LYS A 223 "
        pdb=" HA  LYS A 223 "
      ideal   model   delta    sigma   weight residual
     109.00   74.23   34.77 3.00e+00 1.11e-01 1.34e+02
  angle pdb=" C   LYS A 223 "
        pdb=" CA  LYS A 223 "
        pdb=" HA  LYS A 223 "
      ideal   model   delta    sigma   weight residual
     109.00   74.47   34.53 3.00e+00 1.11e-01 1.32e+02
  angle pdb=" C   LEU C 272 "
        pdb=" CA  LEU C 272 "
        pdb=" HA  LEU C 272 "
      ideal   model   delta    sigma   weight residual
     109.00   74.77   34.23 3.00e+00 1.11e-01 1.30e+02
  ... (remaining 16504 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.01: 4343
       28.01 -    56.02: 77
       56.02 -    84.03: 20
       84.03 -   112.03: 0
      112.03 -   140.04: 6
  Dihedral angle restraints: 4446
    sinusoidal: 2288
      harmonic: 2158
  Sorted by residual:
  dihedral pdb=" C5' ADP A 401 "
           pdb=" O5' ADP A 401 "
           pdb=" PA  ADP A 401 "
           pdb=" O2A ADP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  159.96  140.04     1      2.00e+01 2.50e-03 4.24e+01
  dihedral pdb=" C5' ADP B 401 "
           pdb=" O5' ADP B 401 "
           pdb=" PA  ADP B 401 "
           pdb=" O2A ADP B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  160.15  139.85     1      2.00e+01 2.50e-03 4.23e+01
  dihedral pdb=" O2A ADP A 401 "
           pdb=" O3A ADP A 401 "
           pdb=" PA  ADP A 401 "
           pdb=" PB  ADP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  179.63  120.37     1      2.00e+01 2.50e-03 3.61e+01
  ... (remaining 4443 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 732
       0.084 -    0.168: 45
       0.168 -    0.252: 0
       0.252 -    0.336: 2
       0.336 -    0.420: 3
  Chirality restraints: 782
  Sorted by residual:
  chirality pdb=" CA  PRO A 222 "
            pdb=" N   PRO A 222 "
            pdb=" C   PRO A 222 "
            pdb=" CB  PRO A 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.30    0.42 2.00e-01 2.50e+01 4.41e+00
  chirality pdb=" CA  LEU C 272 "
            pdb=" N   LEU C 272 "
            pdb=" C   LEU C 272 "
            pdb=" CB  LEU C 272 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.25e+00
  chirality pdb=" CA  LYS A 223 "
            pdb=" N   LYS A 223 "
            pdb=" C   LYS A 223 "
            pdb=" CB  LYS A 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.24e+00
  ... (remaining 779 not shown)

  Planarity restraints: 1384
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 285 "    0.010 5.00e-02 4.00e+02   1.46e-02 3.40e-01
        pdb=" N   PRO A 286 "   -0.025 5.00e-02 4.00e+02
        pdb=" CA  PRO A 286 "    0.007 5.00e-02 4.00e+02
        pdb=" CD  PRO A 286 "    0.008 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 285 "    0.009 5.00e-02 4.00e+02   1.44e-02 3.30e-01
        pdb=" N   PRO B 286 "   -0.025 5.00e-02 4.00e+02
        pdb=" CA  PRO B 286 "    0.007 5.00e-02 4.00e+02
        pdb=" CD  PRO B 286 "    0.008 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 247 "    0.009 5.00e-02 4.00e+02   1.39e-02 3.07e-01
        pdb=" N   PRO A 248 "   -0.024 5.00e-02 4.00e+02
        pdb=" CA  PRO A 248 "    0.007 5.00e-02 4.00e+02
        pdb=" CD  PRO A 248 "    0.008 5.00e-02 4.00e+02
  ... (remaining 1381 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.22: 630
        2.22 -     2.82: 18708
        2.82 -     3.41: 21212
        3.41 -     4.01: 27821
        4.01 -     4.60: 43887
  Nonbonded interactions: 112258
  Sorted by model distance:
  nonbonded pdb=" H   LYS A 223 "
            pdb=" HA  LYS A 223 "
     model   vdw
     1.630 1.816
  nonbonded pdb=" O   GLY B  26 "
            pdb=" HG1 THR B  30 "
     model   vdw
     1.698 2.450
  nonbonded pdb=" O   PRO A  43 "
            pdb="HD21 ASN A  78 "
     model   vdw
     1.709 2.450
  nonbonded pdb=" O   GLN C 262 "
            pdb=" H   LEU C 266 "
     model   vdw
     1.710 2.450
  nonbonded pdb=" O   PRO B  43 "
            pdb="HD22 ASN B  78 "
     model   vdw
     1.712 2.450
  ... (remaining 112253 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 94 or resid 99 through 116 or resid 126 through  \ 
131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 133 through 189 or resid 221 through 346 or resid 501))
  selection = (chain 'B' and (resid 1 through 88 or (resid 89 and (name N or name CA or name C \ 
 or name O or name CB or name H or name HA )) or resid 90 through 94 or resid 97 \ 
 through 136 or (resid 137 and (name N or name CA or name C or name O or name CB \ 
 or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or res \ 
id 138 through 184 or (resid 185 and (name N or name CA or name C or name O or n \ 
ame CB or name CG or name CD1 or name CD2 or name H or name HA )) or resid 186 t \ 
hrough 222 or (resid 223 and (name N or name CA or name C or name O or name CB o \ 
r name CG or name CD or name CE or name NZ or name H or name HA )) or resid 224  \ 
through 345 or (resid 346 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 501))
}

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:             2.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.170
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     27.900
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
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      :  0.004   0.108   4972  Z= 0.247
  Angle     :  0.678  13.259   6761  Z= 0.284
  Chirality :  0.045   0.420    782
  Planarity :  0.001   0.015    858
  Dihedral  : 13.617 140.043   1765
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  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: -2.87 (0.31), residues: 579
  helix: -2.00 (0.26), residues: 273
  sheet: -1.96 (0.65), residues: 44
  loop : -1.63 (0.38), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP A 344 
 HIS   0.001   0.000   HIS A  56 
 PHE   0.004   0.001   PHE B  62 
 TYR   0.005   0.001   TYR A 340 
 ARG   0.001   0.000   ARG B 258 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  185 is missing expected H atoms. Skipping.
Residue LYS  223 is missing expected H atoms. Skipping.
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  266 is missing expected H atoms. Skipping.
Residue VAL  267 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue ALA  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue ILE  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue ILE  276 is missing expected H atoms. Skipping.
Residue ILE  277 is missing expected H atoms. Skipping.
Residue ILE  279 is missing expected H atoms. Skipping.
Residue TYR  280 is missing expected H atoms. Skipping.
Evaluate side-chains
  103 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.658 
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  151 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8352 (ttmm)
REVERT: A  165 THR cc_start: 0.9253 (p) cc_final: 0.8964 (t)
REVERT: A  235 ARG cc_start: 0.8303 (ttm110) cc_final: 0.7540 (mtt90)
REVERT: B  151 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8343 (ttmm)
REVERT: B  165 THR cc_start: 0.9217 (p) cc_final: 0.8918 (t)
REVERT: B  183 LYS cc_start: 0.8292 (tppt) cc_final: 0.8045 (ttpt)
REVERT: B  235 ARG cc_start: 0.8219 (ttm110) cc_final: 0.7631 (mtp-110)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.3816
  time to fit residues: 48.9286
Evaluate side-chains
  76 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.120420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.091332 restraints weight = 23427.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.095656 restraints weight = 11600.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.098679 restraints weight = 7495.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4972  Z= 0.261
  Angle     :  0.602   6.433   6761  Z= 0.298
  Chirality :  0.048   0.399    782
  Planarity :  0.004   0.025    858
  Dihedral  : 12.479 151.906    687
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  6.31 %
    Favored  : 92.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.34), residues: 579
  helix: -0.08 (0.29), residues: 294
  sheet: -1.91 (0.64), residues: 44
  loop : -1.16 (0.42), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 144 
 HIS   0.003   0.001   HIS B  56 
 PHE   0.009   0.001   PHE B 174 
 TYR   0.007   0.001   TYR B 340 
 ARG   0.002   0.000   ARG B 295 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  185 is missing expected H atoms. Skipping.
Residue LYS  223 is missing expected H atoms. Skipping.
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  266 is missing expected H atoms. Skipping.
Residue VAL  267 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue ALA  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue ILE  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue ILE  276 is missing expected H atoms. Skipping.
Residue ILE  277 is missing expected H atoms. Skipping.
Residue ILE  279 is missing expected H atoms. Skipping.
Residue TYR  280 is missing expected H atoms. Skipping.
Evaluate side-chains
  82 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 THR cc_start: 0.9401 (p) cc_final: 0.9169 (t)
REVERT: B  144 TRP cc_start: 0.7516 (m100) cc_final: 0.7261 (m100)
REVERT: B  165 THR cc_start: 0.9419 (p) cc_final: 0.9199 (t)
REVERT: B  183 LYS cc_start: 0.8525 (tppt) cc_final: 0.8255 (ttpt)
REVERT: B  268 MET cc_start: 0.8393 (mtm) cc_final: 0.8190 (mtp)
REVERT: B  309 ASP cc_start: 0.8077 (p0) cc_final: 0.7854 (p0)
  outliers start: 4
  outliers final: 3
  residues processed: 80
  average time/residue: 0.2794
  time to fit residues: 29.8299
Evaluate side-chains
  68 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  226 VAL
Chi-restraints excluded: chain B residue   84 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 40 optimal weight:    7.9990
   chunk 59 optimal weight:   10.0000
   chunk 20 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 10 optimal weight:   10.0000
   chunk 55 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 37 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.120152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.091356 restraints weight = 23458.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.095870 restraints weight = 11568.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.098768 restraints weight = 7418.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.3058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4972  Z= 0.167
  Angle     :  0.544   6.184   6761  Z= 0.256
  Chirality :  0.046   0.397    782
  Planarity :  0.003   0.030    858
  Dihedral  : 11.538 140.948    687
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  9.86 %
    Favored  : 89.74 %
  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: -0.03 (0.35), residues: 579
  helix:  0.99 (0.31), residues: 294
  sheet: -1.62 (0.64), residues: 44
  loop : -0.91 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 144 
 HIS   0.001   0.000   HIS B  12 
 PHE   0.013   0.001   PHE B 146 
 TYR   0.010   0.001   TYR B 254 
 ARG   0.001   0.000   ARG B 235 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  185 is missing expected H atoms. Skipping.
Residue LYS  223 is missing expected H atoms. Skipping.
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  266 is missing expected H atoms. Skipping.
Residue VAL  267 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue ALA  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue ILE  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue ILE  276 is missing expected H atoms. Skipping.
Residue ILE  277 is missing expected H atoms. Skipping.
Residue ILE  279 is missing expected H atoms. Skipping.
Residue TYR  280 is missing expected H atoms. Skipping.
Evaluate side-chains
  76 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 THR cc_start: 0.9431 (p) cc_final: 0.9206 (t)
REVERT: B  165 THR cc_start: 0.9456 (p) cc_final: 0.9234 (t)
REVERT: B  183 LYS cc_start: 0.8555 (tppt) cc_final: 0.8341 (ttpt)
  outliers start: 2
  outliers final: 2
  residues processed: 75
  average time/residue: 0.2779
  time to fit residues: 27.9442
Evaluate side-chains
  69 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 67
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain B residue   84 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 35 optimal weight:    0.4980
   chunk 56 optimal weight:    0.2980
   chunk 22 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 10 optimal weight:   10.0000
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.119631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.090895 restraints weight = 23550.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.095375 restraints weight = 11737.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.098160 restraints weight = 7572.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.3483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4972  Z= 0.159
  Angle     :  0.534   5.782   6761  Z= 0.249
  Chirality :  0.046   0.395    782
  Planarity :  0.003   0.030    858
  Dihedral  : 11.516 160.564    687
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 10.85 %
    Favored  : 88.56 %
  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:  0.32 (0.36), residues: 579
  helix:  1.34 (0.31), residues: 294
  sheet: -1.74 (0.61), residues: 48
  loop : -0.75 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 144 
 HIS   0.001   0.000   HIS A   6 
 PHE   0.004   0.001   PHE B  62 
 TYR   0.009   0.001   TYR A 254 
 ARG   0.001   0.000   ARG B 295 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  185 is missing expected H atoms. Skipping.
Residue LYS  223 is missing expected H atoms. Skipping.
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  266 is missing expected H atoms. Skipping.
Residue VAL  267 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue ALA  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue ILE  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue ILE  276 is missing expected H atoms. Skipping.
Residue ILE  277 is missing expected H atoms. Skipping.
Residue ILE  279 is missing expected H atoms. Skipping.
Residue TYR  280 is missing expected H atoms. Skipping.
Evaluate side-chains
  72 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 THR cc_start: 0.9433 (p) cc_final: 0.9199 (t)
REVERT: A  338 LYS cc_start: 0.8168 (pttt) cc_final: 0.7884 (mmmm)
REVERT: B  165 THR cc_start: 0.9456 (p) cc_final: 0.9233 (t)
REVERT: B  183 LYS cc_start: 0.8570 (tppt) cc_final: 0.8331 (ttpt)
  outliers start: 3
  outliers final: 3
  residues processed: 70
  average time/residue: 0.2879
  time to fit residues: 26.9903
Evaluate side-chains
  69 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  140 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 12 optimal weight:    9.9990
   chunk 54 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 38 optimal weight:    0.2980
   chunk 24 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.118829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.089855 restraints weight = 23702.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.094182 restraints weight = 12139.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.097018 restraints weight = 7992.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.3734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4972  Z= 0.162
  Angle     :  0.541   6.258   6761  Z= 0.250
  Chirality :  0.046   0.397    782
  Planarity :  0.003   0.031    858
  Dihedral  : 11.272 171.002    687
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 10.45 %
    Favored  : 88.76 %
  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:  0.53 (0.36), residues: 579
  helix:  1.48 (0.32), residues: 294
  sheet: -1.48 (0.63), residues: 48
  loop : -0.63 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 144 
 HIS   0.001   0.001   HIS B   6 
 PHE   0.004   0.001   PHE B 242 
 TYR   0.009   0.001   TYR B 254 
 ARG   0.001   0.000   ARG B 235 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  185 is missing expected H atoms. Skipping.
Residue LYS  223 is missing expected H atoms. Skipping.
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  266 is missing expected H atoms. Skipping.
Residue VAL  267 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue ALA  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue ILE  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue ILE  276 is missing expected H atoms. Skipping.
Residue ILE  277 is missing expected H atoms. Skipping.
Residue ILE  279 is missing expected H atoms. Skipping.
Residue TYR  280 is missing expected H atoms. Skipping.
Evaluate side-chains
  71 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 TRP cc_start: 0.7705 (m100) cc_final: 0.7350 (m100)
REVERT: A  165 THR cc_start: 0.9439 (p) cc_final: 0.9214 (t)
REVERT: A  338 LYS cc_start: 0.8186 (pttt) cc_final: 0.7961 (mmmm)
REVERT: B  165 THR cc_start: 0.9451 (p) cc_final: 0.9241 (t)
REVERT: B  183 LYS cc_start: 0.8600 (tppt) cc_final: 0.8391 (ttpt)
  outliers start: 4
  outliers final: 2
  residues processed: 68
  average time/residue: 0.2965
  time to fit residues: 26.9668
Evaluate side-chains
  67 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain B residue   84 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 12 optimal weight:    8.9990
   chunk 50 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.117574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.089309 restraints weight = 23730.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.093624 restraints weight = 11707.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.096526 restraints weight = 7558.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.4015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4972  Z= 0.196
  Angle     :  0.548   6.293   6761  Z= 0.257
  Chirality :  0.047   0.398    782
  Planarity :  0.003   0.033    858
  Dihedral  :  9.913 166.605    687
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 11.64 %
    Favored  : 87.77 %
  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:  0.61 (0.36), residues: 579
  helix:  1.53 (0.31), residues: 294
  sheet: -1.31 (0.65), residues: 48
  loop : -0.59 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 144 
 HIS   0.002   0.001   HIS B   6 
 PHE   0.006   0.001   PHE A 277 
 TYR   0.006   0.001   TYR A 254 
 ARG   0.001   0.000   ARG B 258 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  185 is missing expected H atoms. Skipping.
Residue LYS  223 is missing expected H atoms. Skipping.
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  266 is missing expected H atoms. Skipping.
Residue VAL  267 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue ALA  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue ILE  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue ILE  276 is missing expected H atoms. Skipping.
Residue ILE  277 is missing expected H atoms. Skipping.
Residue ILE  279 is missing expected H atoms. Skipping.
Residue TYR  280 is missing expected H atoms. Skipping.
Evaluate side-chains
  69 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 TRP cc_start: 0.7636 (m100) cc_final: 0.7406 (m100)
REVERT: A  165 THR cc_start: 0.9454 (p) cc_final: 0.9222 (t)
REVERT: A  338 LYS cc_start: 0.8181 (pttt) cc_final: 0.7951 (mmmm)
REVERT: B  165 THR cc_start: 0.9473 (p) cc_final: 0.9248 (t)
REVERT: B  183 LYS cc_start: 0.8655 (tppt) cc_final: 0.8446 (ttpt)
  outliers start: 3
  outliers final: 3
  residues processed: 67
  average time/residue: 0.2853
  time to fit residues: 25.6791
Evaluate side-chains
  65 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  140 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 52 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0980
   chunk 12 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0770
   chunk 11 optimal weight:    2.9990
   chunk 15 optimal weight:    0.2980
   chunk 56 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.118252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.089920 restraints weight = 23670.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.094255 restraints weight = 12035.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.097102 restraints weight = 7851.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.4139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4972  Z= 0.116
  Angle     :  0.517   6.354   6761  Z= 0.236
  Chirality :  0.046   0.398    782
  Planarity :  0.003   0.027    858
  Dihedral  :  8.454 132.270    687
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 12.23 %
    Favored  : 87.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.36), residues: 579
  helix:  1.95 (0.32), residues: 295
  sheet: -1.05 (0.67), residues: 48
  loop : -0.45 (0.41), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 144 
 HIS   0.001   0.000   HIS B 271 
 PHE   0.006   0.001   PHE B 146 
 TYR   0.007   0.001   TYR B 254 
 ARG   0.001   0.000   ARG B 235 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  185 is missing expected H atoms. Skipping.
Residue LYS  223 is missing expected H atoms. Skipping.
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  266 is missing expected H atoms. Skipping.
Residue VAL  267 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue ALA  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue ILE  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue ILE  276 is missing expected H atoms. Skipping.
Residue ILE  277 is missing expected H atoms. Skipping.
Residue ILE  279 is missing expected H atoms. Skipping.
Residue TYR  280 is missing expected H atoms. Skipping.
Evaluate side-chains
  65 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 THR cc_start: 0.9440 (p) cc_final: 0.9221 (t)
REVERT: B  165 THR cc_start: 0.9438 (p) cc_final: 0.9221 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 64
  average time/residue: 0.3259
  time to fit residues: 27.5992
Evaluate side-chains
  60 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.117167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.087771 restraints weight = 24342.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.092139 restraints weight = 12128.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.095052 restraints weight = 7914.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.4410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4972  Z= 0.231
  Angle     :  0.555   5.821   6761  Z= 0.262
  Chirality :  0.047   0.400    782
  Planarity :  0.004   0.030    858
  Dihedral  :  8.510 125.712    687
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.62 %
    Favored  : 87.38 %
  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:  0.89 (0.36), residues: 579
  helix:  1.69 (0.31), residues: 294
  sheet: -0.98 (0.69), residues: 48
  loop : -0.41 (0.42), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 144 
 HIS   0.003   0.001   HIS A   6 
 PHE   0.007   0.001   PHE A 277 
 TYR   0.006   0.001   TYR B 332 
 ARG   0.001   0.000   ARG B 293 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  185 is missing expected H atoms. Skipping.
Residue LYS  223 is missing expected H atoms. Skipping.
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  266 is missing expected H atoms. Skipping.
Residue VAL  267 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue ALA  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue ILE  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue ILE  276 is missing expected H atoms. Skipping.
Residue ILE  277 is missing expected H atoms. Skipping.
Residue ILE  279 is missing expected H atoms. Skipping.
Residue TYR  280 is missing expected H atoms. Skipping.
Evaluate side-chains
  59 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 THR cc_start: 0.9450 (p) cc_final: 0.9218 (t)
REVERT: B  165 THR cc_start: 0.9478 (p) cc_final: 0.9251 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.2780
  time to fit residues: 22.8710
Evaluate side-chains
  59 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 44 optimal weight:    0.5980
   chunk 7 optimal weight:    0.1980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.117962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.088739 restraints weight = 23696.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.093224 restraints weight = 11881.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.096038 restraints weight = 7722.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.4553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   4972  Z= 0.148
  Angle     :  0.529   6.563   6761  Z= 0.243
  Chirality :  0.046   0.399    782
  Planarity :  0.003   0.031    858
  Dihedral  :  8.132 119.344    687
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 12.62 %
    Favored  : 87.18 %
  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 (0.36), residues: 579
  helix:  1.94 (0.32), residues: 295
  sheet: -0.85 (0.70), residues: 48
  loop : -0.34 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 144 
 HIS   0.001   0.000   HIS A  56 
 PHE   0.008   0.001   PHE B 146 
 TYR   0.006   0.001   TYR B 254 
 ARG   0.001   0.000   ARG B 235 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  185 is missing expected H atoms. Skipping.
Residue LYS  223 is missing expected H atoms. Skipping.
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  266 is missing expected H atoms. Skipping.
Residue VAL  267 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue ALA  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue ILE  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue ILE  276 is missing expected H atoms. Skipping.
Residue ILE  277 is missing expected H atoms. Skipping.
Residue ILE  279 is missing expected H atoms. Skipping.
Residue TYR  280 is missing expected H atoms. Skipping.
Evaluate side-chains
  62 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 TRP cc_start: 0.7419 (m-10) cc_final: 0.7167 (m-10)
REVERT: A  165 THR cc_start: 0.9460 (p) cc_final: 0.9221 (t)
REVERT: B  165 THR cc_start: 0.9472 (p) cc_final: 0.9236 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 61
  average time/residue: 0.2872
  time to fit residues: 24.0499
Evaluate side-chains
  61 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 60 optimal weight:    9.9990
   chunk 36 optimal weight:    0.7980
   chunk 55 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 35 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 9 optimal weight:    9.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.117890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.089445 restraints weight = 23946.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.093724 restraints weight = 12166.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.096546 restraints weight = 7938.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.4576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   4972  Z= 0.141
  Angle     :  0.525   5.864   6761  Z= 0.242
  Chirality :  0.046   0.398    782
  Planarity :  0.003   0.030    858
  Dihedral  :  7.801 111.400    687
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.21 %
    Favored  : 86.79 %
  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:  1.23 (0.36), residues: 579
  helix:  2.00 (0.31), residues: 301
  sheet: -0.73 (0.70), residues: 48
  loop : -0.39 (0.43), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 144 
 HIS   0.001   0.000   HIS A  56 
 PHE   0.007   0.001   PHE B 146 
 TYR   0.006   0.001   TYR B 254 
 ARG   0.001   0.000   ARG B 235 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  185 is missing expected H atoms. Skipping.
Residue LYS  223 is missing expected H atoms. Skipping.
Residue VAL  184 is missing expected H atoms. Skipping.
Residue LEU  266 is missing expected H atoms. Skipping.
Residue VAL  267 is missing expected H atoms. Skipping.
Residue ILE  270 is missing expected H atoms. Skipping.
Residue ALA  271 is missing expected H atoms. Skipping.
Residue LEU  272 is missing expected H atoms. Skipping.
Residue ILE  273 is missing expected H atoms. Skipping.
Residue LEU  274 is missing expected H atoms. Skipping.
Residue LEU  275 is missing expected H atoms. Skipping.
Residue ILE  276 is missing expected H atoms. Skipping.
Residue ILE  277 is missing expected H atoms. Skipping.
Residue ILE  279 is missing expected H atoms. Skipping.
Residue TYR  280 is missing expected H atoms. Skipping.
Evaluate side-chains
  62 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 TRP cc_start: 0.7296 (m-10) cc_final: 0.7032 (m-10)
REVERT: A  165 THR cc_start: 0.9440 (p) cc_final: 0.9224 (t)
REVERT: B  165 THR cc_start: 0.9446 (p) cc_final: 0.9231 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.2809
  time to fit residues: 23.7332
Evaluate side-chains
  61 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0470
   chunk 51 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.6278

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.118332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.090114 restraints weight = 23580.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.094518 restraints weight = 12013.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.097282 restraints weight = 7817.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.4716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   4972  Z= 0.136
  Angle     :  0.522   5.677   6761  Z= 0.239
  Chirality :  0.046   0.398    782
  Planarity :  0.003   0.030    858
  Dihedral  :  7.387 102.677    687
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.21 %
    Favored  : 86.79 %
  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:  1.43 (0.37), residues: 579
  helix:  2.18 (0.31), residues: 301
  sheet: -0.47 (0.71), residues: 48
  loop : -0.37 (0.43), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 144 
 HIS   0.001   0.000   HIS A  56 
 PHE   0.007   0.001   PHE B 146 
 TYR   0.006   0.001   TYR B 254 
 ARG   0.001   0.000   ARG B 235 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3121.04 seconds
wall clock time: 54 minutes 3.43 seconds (3243.43 seconds total)