Starting phenix.real_space_refine
on Thu Jul 31 02:20:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ozs_13134/07_2025/7ozs_13134.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ozs_13134/07_2025/7ozs_13134.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ozs_13134/07_2025/7ozs_13134.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ozs_13134/07_2025/7ozs_13134.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ozs_13134/07_2025/7ozs_13134.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ozs_13134/07_2025/7ozs_13134.cif"
  }
  resolution = 3.5
  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=   0.013 sd=   0.083
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 102 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     119      5.49       5
     S      38      5.16       5
     C    7615      2.51       5
     N    2272      2.21       5
     O    2726      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12770
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "B"
      Number of atoms: 1147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1147
          Classifications: {'peptide': 141}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 136}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 2166
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2166
          Classifications: {'peptide': 275}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 6, 'TRANS': 268}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 76
          Unresolved non-hydrogen angles: 92
          Unresolved non-hydrogen dihedrals: 60
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 44
    Chain: "D"
      Number of atoms: 641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 641
          Classifications: {'peptide': 88}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 13, 'TRANS': 74}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "C"
      Number of atoms: 1901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1901
          Classifications: {'peptide': 239}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 16, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "3"
      Number of atoms: 2536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 2536
          Classifications: {'RNA': 119}
          Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 55, 'rna3p_pyr': 54}
          Link IDs: {'rna2p': 10, 'rna3p': 108}
    Chain: "E"
      Number of atoms: 115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 115
          Classifications: {'peptide': 23}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'TRANS': 22}
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'UNK:plan-1': 23}
          Unresolved non-hydrogen planarities: 23
    Chain: "F"
      Number of atoms: 4264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 571, 4264
          Classifications: {'peptide': 571}
          Incomplete info: {'truncation_to_alanine': 57}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 544}
          Chain breaks: 4
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 179
          Unresolved non-hydrogen angles: 224
          Unresolved non-hydrogen dihedrals: 139
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 11}
          Unresolved non-hydrogen planarities: 79
  Time building chain proxies: 7.62, per 1000 atoms: 0.60
  Number of scatterers: 12770
  At special positions: 0
  Unit cell: (88.956, 119.667, 146.142, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      38     16.00
     P     119     15.00
     O    2726      8.00
     N    2272      7.00
     C    7615      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.02
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2536

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 7 sheets defined
      58.3% alpha, 8.8% beta
      33 base pairs and 78 stacking pairs defined.
    Time for finding SS restraints: 4.24
  Creating SS restraints...
    Processing helix  chain 'B' and resid 8 through 12
      removed outlier: 3.762A  pdb=" N   GLU B  12 " --> pdb=" O   PRO B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 43
      removed outlier: 3.737A  pdb=" N   LYS B  36 " --> pdb=" O   THR B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 88
      removed outlier: 4.171A  pdb=" N   GLU B  78 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLU B  79 " --> pdb=" O   PRO B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 97
      No H-bonds generated for 'chain 'B' and resid 95 through 97'
    Processing helix  chain 'B' and resid 136 through 141
      removed outlier: 3.788A  pdb=" N   VAL B 139 " --> pdb=" O   GLY B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 168
      removed outlier: 3.813A  pdb=" N   PHE B 168 " --> pdb=" O   PHE B 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 20 through 25
    Processing helix  chain 'A' and resid 29 through 40
    Processing helix  chain 'A' and resid 81 through 86
    Processing helix  chain 'A' and resid 94 through 113
    Processing helix  chain 'A' and resid 160 through 173
      removed outlier: 3.697A  pdb=" N   GLY A 164 " --> pdb=" O   ALA A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 203
      removed outlier: 3.605A  pdb=" N   TYR A 203 " --> pdb=" O   LYS A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 217
    Processing helix  chain 'A' and resid 219 through 225
    Processing helix  chain 'A' and resid 226 through 232
    Processing helix  chain 'A' and resid 235 through 253
    Processing helix  chain 'A' and resid 267 through 276
    Processing helix  chain 'A' and resid 283 through 298
    Processing helix  chain 'D' and resid 43 through 69
      removed outlier: 4.058A  pdb=" N   LEU D  47 " --> pdb=" O   ASP D  43 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   THR D  69 " --> pdb=" O   GLN D  65 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 12 through 20
    Processing helix  chain 'C' and resid 39 through 53
    Processing helix  chain 'C' and resid 72 through 83
    Processing helix  chain 'C' and resid 125 through 129
      removed outlier: 3.538A  pdb=" N   GLN C 128 " --> pdb=" O   SER C 125 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   PHE C 129 " --> pdb=" O   ILE C 126 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 125 through 129'
    Processing helix  chain 'C' and resid 148 through 150
      No H-bonds generated for 'chain 'C' and resid 148 through 150'
    Processing helix  chain 'C' and resid 155 through 169
      removed outlier: 4.014A  pdb=" N   ASP C 166 " --> pdb=" O   SER C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 264 through 272
    Processing helix  chain 'E' and resid 9 through 17
      removed outlier: 4.049A  pdb=" N   UNK E  15 " --> pdb=" O   UNK E  12 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   UNK E  17 " --> pdb=" O   UNK E  14 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 35 through 44
    Processing helix  chain 'F' and resid 47 through 64
      removed outlier: 3.988A  pdb=" N   GLY F  56 " --> pdb=" O   THR F  52 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ALA F  57 " --> pdb=" O   THR F  53 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ASP F  64 " --> pdb=" O   ASN F  60 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 67 through 74
    Processing helix  chain 'F' and resid 75 through 83
    Processing helix  chain 'F' and resid 89 through 107
      removed outlier: 3.598A  pdb=" N   ARG F  93 " --> pdb=" O   ASN F  89 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 108 through 118
      removed outlier: 3.898A  pdb=" N   CYS F 112 " --> pdb=" O   GLU F 108 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 119 through 137
      removed outlier: 4.171A  pdb=" N   ALA F 123 " --> pdb=" O   ASP F 119 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   THR F 137 " --> pdb=" O   GLU F 133 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 146 through 169
    Processing helix  chain 'F' and resid 171 through 181
      removed outlier: 3.577A  pdb=" N   LYS F 181 " --> pdb=" O   ALA F 177 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 181 through 195
      removed outlier: 4.056A  pdb=" N   LEU F 185 " --> pdb=" O   LYS F 181 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ASP F 195 " --> pdb=" O   LEU F 191 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 198 through 213
    Processing helix  chain 'F' and resid 216 through 225
    Processing helix  chain 'F' and resid 230 through 241
    Processing helix  chain 'F' and resid 245 through 260
      removed outlier: 3.957A  pdb=" N   ALA F 249 " --> pdb=" O   ARG F 245 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLY F 251 " --> pdb=" O   VAL F 247 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   VAL F 252 " --> pdb=" O   MET F 248 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 277 through 288
      removed outlier: 3.873A  pdb=" N   LEU F 281 " --> pdb=" O   LEU F 277 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 302 through 329
      removed outlier: 4.391A  pdb=" N   GLN F 320 " --> pdb=" O   GLY F 316 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   GLU F 321 " --> pdb=" O   THR F 317 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLY F 329 " --> pdb=" O   LYS F 325 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 389 through 399
    Processing helix  chain 'F' and resid 411 through 420
    Processing helix  chain 'F' and resid 420 through 430
    Processing helix  chain 'F' and resid 435 through 458
    Processing helix  chain 'F' and resid 461 through 465
      removed outlier: 3.777A  pdb=" N   GLY F 464 " --> pdb=" O   PHE F 461 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 466 through 484
      Proline residue:  F 475  - end of helix
    Processing helix  chain 'F' and resid 484 through 491
      removed outlier: 3.647A  pdb=" N   ALA F 491 " --> pdb=" O   PRO F 487 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 496 through 514
      removed outlier: 3.874A  pdb=" N   VAL F 512 " --> pdb=" O   ALA F 508 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 522 through 535
      removed outlier: 3.682A  pdb=" N   LYS F 526 " --> pdb=" O   ASN F 522 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LYS F 535 " --> pdb=" O   TYR F 531 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 550 through 553
      removed outlier: 3.780A  pdb=" N   GLN F 553 " --> pdb=" O   ASP F 550 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 550 through 553'
    Processing helix  chain 'F' and resid 554 through 567
      removed outlier: 3.578A  pdb=" N   LYS F 558 " --> pdb=" O   GLY F 554 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   ALA F 567 " --> pdb=" O   VAL F 563 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 572 through 589
      removed outlier: 3.511A  pdb=" N   ASN F 576 " --> pdb=" O   PRO F 572 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 594 through 609
    Processing helix  chain 'F' and resid 614 through 620
      removed outlier: 4.171A  pdb=" N   LYS F 618 " --> pdb=" O   LEU F 614 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 625 through 644
      removed outlier: 3.912A  pdb=" N   HIS F 629 " --> pdb=" O   GLY F 625 " (cutoff:3.500A)
      Proline residue:  F 635  - end of helix
    Processing helix  chain 'F' and resid 649 through 674
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 48
      removed outlier: 6.936A  pdb=" N   CYS B 131 " --> pdb=" O   GLN B  16 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   LEU B  18 " --> pdb=" O   TYR B 129 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   TYR B 129 " --> pdb=" O   LEU B  18 " (cutoff:3.500A)
      removed outlier: 4.762A  pdb=" N   LEU B  20 " --> pdb=" O   ASP B 127 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   ASP B 127 " --> pdb=" O   LEU B  20 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 91 through 93
      removed outlier: 6.983A  pdb=" N   LEU B  92 " --> pdb=" O   ARG B 173 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 52
    Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55
    Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 67
    Processing sheet with id=AA6, first strand: chain 'D' and resid 22 through 24
      removed outlier: 6.705A  pdb=" N   MET C 141 " --> pdb=" O   VAL C 185 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   VAL C 187 " --> pdb=" O   MET C 141 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   VAL C 143 " --> pdb=" O   VAL C 187 " (cutoff:3.500A)
      removed outlier: 8.155A  pdb=" N   ALA C 189 " --> pdb=" O   VAL C 143 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   ALA C 145 " --> pdb=" O   ALA C 189 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   LEU C 225 " --> pdb=" O   MET C 253 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   MET C 253 " --> pdb=" O   LEU C 225 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   LEU C 227 " --> pdb=" O   PRO C 251 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   VAL C 229 " --> pdb=" O   HIS C 249 " (cutoff:3.500A)
      removed outlier: 5.492A  pdb=" N   GLU C 115 " --> pdb=" O   GLY C 258 " (cutoff:3.500A)
      removed outlier: 4.957A  pdb=" N   MET C 260 " --> pdb=" O   MET C 113 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   MET C 113 " --> pdb=" O   MET C 260 " (cutoff:3.500A)
      removed outlier: 5.231A  pdb=" N   VAL C 110 " --> pdb=" O   PHE C 106 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   PHE C 106 " --> pdb=" O   VAL C 110 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   LEU C  31 " --> pdb=" O   VAL C  88 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   GLY C  90 " --> pdb=" O   LEU C  31 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   LEU C  33 " --> pdb=" O   GLY C  90 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 71 through 72

    557 hydrogen bonds defined for protein.
    1602 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      83 hydrogen bonds
      158 hydrogen bond angles
      0 basepair planarities
      33 basepair parallelities
      78 stacking parallelities
  Total time for adding SS restraints: 4.22

  Time building geometry restraints manager: 3.59 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2952
        1.33 -     1.45: 3202
        1.45 -     1.57: 6794
        1.57 -     1.69: 238
        1.69 -     1.81: 61
  Bond restraints: 13247
  Sorted by residual:
  bond pdb=" CA  GLY D  78 "
       pdb=" C   GLY D  78 "
    ideal  model  delta    sigma   weight residual
    1.520  1.504  0.016 7.30e-03 1.88e+04 4.84e+00
  bond pdb=" CA  ALA F 571 "
       pdb=" CB  ALA F 571 "
    ideal  model  delta    sigma   weight residual
    1.537  1.508  0.030 1.47e-02 4.63e+03 4.04e+00
  bond pdb=" CB  GLN B 166 "
       pdb=" CG  GLN B 166 "
    ideal  model  delta    sigma   weight residual
    1.520  1.576 -0.056 3.00e-02 1.11e+03 3.52e+00
  bond pdb=" CB  LYS B  86 "
       pdb=" CG  LYS B  86 "
    ideal  model  delta    sigma   weight residual
    1.520  1.568 -0.048 3.00e-02 1.11e+03 2.61e+00
  bond pdb=" CA  ASP F 550 "
       pdb=" C   ASP F 550 "
    ideal  model  delta    sigma   weight residual
    1.525  1.558 -0.033 2.10e-02 2.27e+03 2.53e+00
  ... (remaining 13242 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.77: 18247
        2.77 -     5.54: 223
        5.54 -     8.30: 37
        8.30 -    11.07: 9
       11.07 -    13.84: 2
  Bond angle restraints: 18518
  Sorted by residual:
  angle pdb=" N   ALA F 571 "
        pdb=" CA  ALA F 571 "
        pdb=" C   ALA F 571 "
      ideal   model   delta    sigma   weight residual
     108.22   99.47    8.75 9.00e-01 1.23e+00 9.45e+01
  angle pdb=" C   PRO F 140 "
        pdb=" N   PRO F 141 "
        pdb=" CA  PRO F 141 "
      ideal   model   delta    sigma   weight residual
     127.00  140.84  -13.84 2.40e+00 1.74e-01 3.33e+01
  angle pdb=" C   ASP F 569 "
        pdb=" N   PRO F 570 "
        pdb=" CA  PRO F 570 "
      ideal   model   delta    sigma   weight residual
     119.83  113.63    6.20 1.08e+00 8.57e-01 3.29e+01
  angle pdb=" C   PRO F 140 "
        pdb=" N   PRO F 141 "
        pdb=" CD  PRO F 141 "
      ideal   model   delta    sigma   weight residual
     120.60  109.00   11.60 2.20e+00 2.07e-01 2.78e+01
  angle pdb=" CB  LYS B  86 "
        pdb=" CG  LYS B  86 "
        pdb=" CD  LYS B  86 "
      ideal   model   delta    sigma   weight residual
     111.30  121.52  -10.22 2.30e+00 1.89e-01 1.98e+01
  ... (remaining 18513 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.80: 7764
       31.80 -    63.61: 370
       63.61 -    95.41: 90
       95.41 -   127.21: 2
      127.21 -   159.02: 1
  Dihedral angle restraints: 8227
    sinusoidal: 4336
      harmonic: 3891
  Sorted by residual:
  dihedral pdb=" CA  ASN A  70 "
           pdb=" C   ASN A  70 "
           pdb=" N   GLY A  71 "
           pdb=" CA  GLY A  71 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.62   27.38     0      5.00e+00 4.00e-02 3.00e+01
  dihedral pdb=" CA  THR A  56 "
           pdb=" C   THR A  56 "
           pdb=" N   ASN A  57 "
           pdb=" CA  ASN A  57 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.23   21.77     0      5.00e+00 4.00e-02 1.90e+01
  dihedral pdb=" C4'   G 3  52 "
           pdb=" C3'   G 3  52 "
           pdb=" O3'   G 3  52 "
           pdb=" P     U 3  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   60.98  159.02     1      3.50e+01 8.16e-04 1.52e+01
  ... (remaining 8224 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1943
       0.065 -    0.129: 246
       0.129 -    0.194: 30
       0.194 -    0.259: 6
       0.259 -    0.324: 5
  Chirality restraints: 2230
  Sorted by residual:
  chirality pdb=" C3'   G 3  52 "
            pdb=" C4'   G 3  52 "
            pdb=" O3'   G 3  52 "
            pdb=" C2'   G 3  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.15   -0.32 2.00e-01 2.50e+01 2.62e+00
  chirality pdb=" CA  LEU F 566 "
            pdb=" N   LEU F 566 "
            pdb=" C   LEU F 566 "
            pdb=" CB  LEU F 566 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.23e+00
  chirality pdb=" CB  ILE B  15 "
            pdb=" CA  ILE B  15 "
            pdb=" CG1 ILE B  15 "
            pdb=" CG2 ILE B  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 1.97e+00
  ... (remaining 2227 not shown)

  Planarity restraints: 1937
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F 563 "   -0.016 2.00e-02 2.50e+03   3.15e-02 9.93e+00
        pdb=" C   VAL F 563 "    0.055 2.00e-02 2.50e+03
        pdb=" O   VAL F 563 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   GLY F 564 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP F 569 "    0.048 5.00e-02 4.00e+02   7.29e-02 8.50e+00
        pdb=" N   PRO F 570 "   -0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO F 570 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO F 570 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 134 "    0.040 5.00e-02 4.00e+02   6.05e-02 5.86e+00
        pdb=" N   PRO C 135 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO C 135 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO C 135 "    0.033 5.00e-02 4.00e+02
  ... (remaining 1934 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 3340
        2.81 -     3.33: 11346
        3.33 -     3.85: 22371
        3.85 -     4.38: 25127
        4.38 -     4.90: 40074
  Nonbonded interactions: 102258
  Sorted by model distance:
  nonbonded pdb=" O   LEU F 132 "
            pdb=" OG1 THR F 136 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OG1 THR A  62 "
            pdb=" O   ALA A  78 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O2'   G 3  76 "
            pdb=" O6    G 3 100 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" OD2 ASP C  48 "
            pdb=" OH  TYR C 123 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" O   GLU F 416 "
            pdb=" OG1 THR F 420 "
     model   vdw
     2.325 3.040
  ... (remaining 102253 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     32.560
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
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   0.056  13247  Z= 0.199
  Angle     :  0.795  13.842  18518  Z= 0.426
  Chirality :  0.046   0.324   2230
  Planarity :  0.006   0.073   1937
  Dihedral  : 17.904 159.017   5691
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  0.87 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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: -1.44 (0.21), residues: 1282
  helix: -0.69 (0.17), residues: 688
  sheet: -0.10 (0.47), residues: 131
  loop : -1.41 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP F 154 
 HIS   0.004   0.001   HIS A 206 
 PHE   0.015   0.002   PHE A 163 
 TYR   0.018   0.001   TYR A 201 
 ARG   0.009   0.000   ARG B 173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17479 (  640)
  hydrogen bonds       : angle       6.62450 ( 1760)
  covalent geometry    : bond        0.00385 (13247)
  covalent geometry    : angle       0.79451 (18518)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 82
  time to evaluate  : 1.324 
Fit side-chains
REVERT: D   48 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7921 (tp30)
REVERT: D   79 VAL cc_start: 0.8810 (t) cc_final: 0.8425 (p)
  outliers start: 3
  outliers final: 1
  residues processed: 85
  average time/residue: 0.2187
  time to fit residues: 29.2938
Evaluate side-chains
  58 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 119 optimal weight:    3.9990
   chunk 107 optimal weight:    5.9990
   chunk 59 optimal weight:    4.9990
   chunk 36 optimal weight:    7.9990
   chunk 72 optimal weight:    6.9990
   chunk 57 optimal weight:    4.9990
   chunk 111 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0050
   chunk 67 optimal weight:    0.9990
   chunk 82 optimal weight:   10.0000
   chunk 128 optimal weight:    8.9990
   overall best weight:    2.6002

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

Flipped N/Q/H residues before XYZ refinement:
C  93 ASN
** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.060316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.043548 restraints weight = 55634.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.045281 restraints weight = 25288.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.046356 restraints weight = 16320.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.1254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13247  Z= 0.185
  Angle     :  0.573   7.108  18518  Z= 0.298
  Chirality :  0.038   0.213   2230
  Planarity :  0.004   0.052   1937
  Dihedral  : 18.377 172.083   3319
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  6.44 %
    Favored  : 92.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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:  0.37 (0.23), residues: 1282
  helix:  1.16 (0.19), residues: 704
  sheet: -0.05 (0.46), residues: 139
  loop : -1.11 (0.27), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP F 473 
 HIS   0.004   0.001   HIS A 206 
 PHE   0.014   0.001   PHE F 461 
 TYR   0.018   0.001   TYR F 474 
 ARG   0.004   0.000   ARG B 173 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04300 (  640)
  hydrogen bonds       : angle       4.18116 ( 1760)
  covalent geometry    : bond        0.00388 (13247)
  covalent geometry    : angle       0.57326 (18518)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 1.229 
Fit side-chains
REVERT: A  166 MET cc_start: 0.8636 (tmm) cc_final: 0.8344 (tmm)
REVERT: D   48 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8283 (tp30)
REVERT: D   93 GLU cc_start: 0.7488 (tm-30) cc_final: 0.6809 (tm-30)
REVERT: D   94 LYS cc_start: 0.8557 (mttp) cc_final: 0.8346 (mptt)
  outliers start: 7
  outliers final: 5
  residues processed: 70
  average time/residue: 0.1961
  time to fit residues: 22.4796
Evaluate side-chains
  64 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 1.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 GLN
Chi-restraints excluded: chain D residue   23 PHE
Chi-restraints excluded: chain C residue   64 ASN
Chi-restraints excluded: chain C residue   93 ASN
Chi-restraints excluded: chain C residue  134 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 101 optimal weight:    9.9990
   chunk 55 optimal weight:    9.9990
   chunk 114 optimal weight:   10.0000
   chunk 89 optimal weight:   40.0000
   chunk 5 optimal weight:    6.9990
   chunk 66 optimal weight:    2.9990
   chunk 73 optimal weight:    8.9990
   chunk 8 optimal weight:    6.9990
   chunk 113 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   chunk 118 optimal weight:    8.9990
   overall best weight:    3.6586

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
A  63 GLN
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.059286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.042322 restraints weight = 56272.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.044024 restraints weight = 25779.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.045094 restraints weight = 16764.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  13247  Z= 0.241
  Angle     :  0.588   6.818  18518  Z= 0.302
  Chirality :  0.038   0.216   2230
  Planarity :  0.004   0.050   1937
  Dihedral  : 18.372 174.707   3319
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  8.56 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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:  1.05 (0.24), residues: 1282
  helix:  1.81 (0.20), residues: 701
  sheet:  0.03 (0.46), residues: 136
  loop : -0.88 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A  95 
 HIS   0.006   0.001   HIS A 206 
 PHE   0.015   0.001   PHE A 163 
 TYR   0.021   0.001   TYR A 201 
 ARG   0.004   0.000   ARG A 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04068 (  640)
  hydrogen bonds       : angle       3.98515 ( 1760)
  covalent geometry    : bond        0.00510 (13247)
  covalent geometry    : angle       0.58791 (18518)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 1.188 
Fit side-chains
REVERT: A  166 MET cc_start: 0.8636 (tmm) cc_final: 0.8387 (tmm)
REVERT: D   93 GLU cc_start: 0.7432 (tm-30) cc_final: 0.6899 (tm-30)
REVERT: D   94 LYS cc_start: 0.8692 (mttp) cc_final: 0.8375 (mptt)
REVERT: F  248 MET cc_start: 0.9191 (mtp) cc_final: 0.8856 (mpp)
REVERT: F  273 CYS cc_start: 0.7948 (p) cc_final: 0.7531 (m)
REVERT: F  474 TYR cc_start: 0.8223 (t80) cc_final: 0.7941 (t80)
  outliers start: 15
  outliers final: 10
  residues processed: 69
  average time/residue: 0.2036
  time to fit residues: 22.8920
Evaluate side-chains
  65 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 1.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   23 PHE
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain C residue   64 ASN
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  249 HIS
Chi-restraints excluded: chain F residue  637 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   chunk 63 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   chunk 141 optimal weight:   10.0000
   chunk 50 optimal weight:    7.9990
   chunk 130 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   chunk 78 optimal weight:    8.9990
   chunk 45 optimal weight:    7.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 182 GLN
F 466 ASN
F 470 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.057815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.040878 restraints weight = 56610.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.042460 restraints weight = 27466.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.043441 restraints weight = 18396.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.057  13247  Z= 0.393
  Angle     :  0.706   8.246  18518  Z= 0.362
  Chirality :  0.043   0.234   2230
  Planarity :  0.005   0.049   1937
  Dihedral  : 18.397 173.987   3316
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 10.19 %
    Favored  : 87.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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:  0.95 (0.24), residues: 1282
  helix:  1.78 (0.20), residues: 702
  sheet: -0.17 (0.45), residues: 136
  loop : -0.97 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  95 
 HIS   0.009   0.001   HIS A 206 
 PHE   0.023   0.002   PHE A 163 
 TYR   0.021   0.002   TYR A 201 
 ARG   0.004   0.001   ARG B 144 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04630 (  640)
  hydrogen bonds       : angle       4.33291 ( 1760)
  covalent geometry    : bond        0.00829 (13247)
  covalent geometry    : angle       0.70584 (18518)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 56
  time to evaluate  : 1.180 
Fit side-chains
REVERT: A  166 MET cc_start: 0.8647 (tmm) cc_final: 0.8262 (tmm)
REVERT: C  108 TYR cc_start: 0.8668 (m-10) cc_final: 0.8452 (m-80)
REVERT: F  248 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8948 (mpp)
REVERT: F  273 CYS cc_start: 0.8104 (p) cc_final: 0.7554 (m)
  outliers start: 22
  outliers final: 16
  residues processed: 72
  average time/residue: 0.1840
  time to fit residues: 22.1905
Evaluate side-chains
  69 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 52
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   23 PHE
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   64 ASN
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  249 HIS
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue  248 MET
Chi-restraints excluded: chain F residue  514 HIS
Chi-restraints excluded: chain F residue  637 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 116 optimal weight:    0.8980
   chunk 128 optimal weight:    0.9990
   chunk 99 optimal weight:    8.9990
   chunk 120 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 92 optimal weight:    5.9990
   chunk 134 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 83 optimal weight:   20.0000
   chunk 119 optimal weight:    6.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A  70 ASN
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  56 HIS
** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.059361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.042431 restraints weight = 55927.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.044146 restraints weight = 25580.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.045224 restraints weight = 16610.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13247  Z= 0.157
  Angle     :  0.543   7.302  18518  Z= 0.280
  Chirality :  0.037   0.211   2230
  Planarity :  0.004   0.051   1937
  Dihedral  : 18.424 169.445   3316
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 12.02 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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:  1.31 (0.24), residues: 1282
  helix:  2.09 (0.20), residues: 708
  sheet: -0.07 (0.46), residues: 136
  loop : -0.87 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 270 
 HIS   0.006   0.001   HIS A  81 
 PHE   0.011   0.001   PHE C 129 
 TYR   0.018   0.001   TYR F 474 
 ARG   0.003   0.000   ARG A  84 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03732 (  640)
  hydrogen bonds       : angle       3.86097 ( 1760)
  covalent geometry    : bond        0.00331 (13247)
  covalent geometry    : angle       0.54342 (18518)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 1.213 
Fit side-chains
REVERT: A  166 MET cc_start: 0.8636 (tmm) cc_final: 0.8243 (tmm)
REVERT: D   93 GLU cc_start: 0.7385 (tm-30) cc_final: 0.7092 (tm-30)
REVERT: D   94 LYS cc_start: 0.8655 (mttp) cc_final: 0.8405 (mttp)
REVERT: F  160 LEU cc_start: 0.9701 (OUTLIER) cc_final: 0.9433 (mm)
REVERT: F  248 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8926 (mpp)
REVERT: F  273 CYS cc_start: 0.8055 (p) cc_final: 0.7558 (m)
  outliers start: 18
  outliers final: 13
  residues processed: 74
  average time/residue: 0.1949
  time to fit residues: 23.4665
Evaluate side-chains
  71 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 ILE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain D residue   23 PHE
Chi-restraints excluded: chain C residue   64 ASN
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain F residue  160 LEU
Chi-restraints excluded: chain F residue  243 ASP
Chi-restraints excluded: chain F residue  248 MET
Chi-restraints excluded: chain F residue  514 HIS
Chi-restraints excluded: chain F residue  637 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 119 optimal weight:    5.9990
   chunk 106 optimal weight:    8.9990
   chunk 14 optimal weight:   20.0000
   chunk 99 optimal weight:    0.9990
   chunk 91 optimal weight:    6.9990
   chunk 138 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0770
   chunk 49 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    3.2146

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

Flipped N/Q/H residues before XYZ refinement:
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.058981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.041977 restraints weight = 56786.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.043668 restraints weight = 26117.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.044702 restraints weight = 17044.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  13247  Z= 0.212
  Angle     :  0.572   9.410  18518  Z= 0.292
  Chirality :  0.038   0.229   2230
  Planarity :  0.004   0.050   1937
  Dihedral  : 18.381 163.788   3316
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 12.79 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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:  1.42 (0.24), residues: 1282
  helix:  2.16 (0.20), residues: 707
  sheet: -0.20 (0.45), residues: 142
  loop : -0.71 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 270 
 HIS   0.005   0.001   HIS A 206 
 PHE   0.014   0.001   PHE A 163 
 TYR   0.032   0.001   TYR C 108 
 ARG   0.003   0.000   ARG A 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03796 (  640)
  hydrogen bonds       : angle       3.88575 ( 1760)
  covalent geometry    : bond        0.00450 (13247)
  covalent geometry    : angle       0.57170 (18518)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 57
  time to evaluate  : 1.259 
Fit side-chains
REVERT: A  166 MET cc_start: 0.8646 (tmm) cc_final: 0.8223 (tmm)
REVERT: D   94 LYS cc_start: 0.8627 (mttp) cc_final: 0.8401 (mttt)
REVERT: C  177 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.7692 (p0)
REVERT: F  160 LEU cc_start: 0.9700 (OUTLIER) cc_final: 0.9429 (mm)
REVERT: F  248 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8969 (mpp)
REVERT: F  273 CYS cc_start: 0.8129 (p) cc_final: 0.7595 (m)
  outliers start: 26
  outliers final: 19
  residues processed: 78
  average time/residue: 0.1903
  time to fit residues: 24.3582
Evaluate side-chains
  78 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 56
  time to evaluate  : 1.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 ILE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain D residue   23 PHE
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   64 ASN
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  177 ASP
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  249 HIS
Chi-restraints excluded: chain F residue  160 LEU
Chi-restraints excluded: chain F residue  243 ASP
Chi-restraints excluded: chain F residue  248 MET
Chi-restraints excluded: chain F residue  514 HIS
Chi-restraints excluded: chain F residue  637 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 131 optimal weight:    9.9990
   chunk 60 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0570
   chunk 120 optimal weight:    9.9990
   chunk 43 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9980
   chunk 102 optimal weight:    8.9990
   chunk 27 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.4902

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

Flipped N/Q/H residues before XYZ refinement:
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.060025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.043165 restraints weight = 56338.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.044887 restraints weight = 25564.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.045962 restraints weight = 16558.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13247  Z= 0.125
  Angle     :  0.522  10.236  18518  Z= 0.267
  Chirality :  0.036   0.226   2230
  Planarity :  0.004   0.050   1937
  Dihedral  : 18.423 160.842   3316
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 13.37 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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:  1.64 (0.24), residues: 1282
  helix:  2.31 (0.20), residues: 707
  sheet: -0.01 (0.46), residues: 134
  loop : -0.60 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 270 
 HIS   0.004   0.001   HIS F 470 
 PHE   0.010   0.001   PHE C 106 
 TYR   0.012   0.001   TYR C 108 
 ARG   0.002   0.000   ARG A 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03376 (  640)
  hydrogen bonds       : angle       3.63740 ( 1760)
  covalent geometry    : bond        0.00266 (13247)
  covalent geometry    : angle       0.52239 (18518)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 57
  time to evaluate  : 1.374 
Fit side-chains
REVERT: A  166 MET cc_start: 0.8614 (tmm) cc_final: 0.8187 (tmm)
REVERT: D   93 GLU cc_start: 0.7392 (tm-30) cc_final: 0.5878 (tm-30)
REVERT: F  160 LEU cc_start: 0.9681 (OUTLIER) cc_final: 0.9399 (mm)
REVERT: F  248 MET cc_start: 0.9142 (mtp) cc_final: 0.8931 (mpp)
REVERT: F  273 CYS cc_start: 0.8136 (p) cc_final: 0.7628 (m)
REVERT: F  637 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8197 (tmm)
  outliers start: 20
  outliers final: 15
  residues processed: 74
  average time/residue: 0.1973
  time to fit residues: 23.9334
Evaluate side-chains
  73 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 56
  time to evaluate  : 1.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 ILE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain D residue   23 PHE
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain C residue   64 ASN
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  249 HIS
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue  160 LEU
Chi-restraints excluded: chain F residue  243 ASP
Chi-restraints excluded: chain F residue  637 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 79 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 9 optimal weight:    7.9990
   chunk 84 optimal weight:   10.0000
   chunk 130 optimal weight:    7.9990
   chunk 57 optimal weight:    7.9990
   chunk 89 optimal weight:   40.0000
   chunk 66 optimal weight:    0.8980
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.059015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.041978 restraints weight = 56350.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.043665 restraints weight = 26176.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.044718 restraints weight = 17121.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.2447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  13247  Z= 0.234
  Angle     :  0.586  10.705  18518  Z= 0.298
  Chirality :  0.038   0.248   2230
  Planarity :  0.004   0.050   1937
  Dihedral  : 18.359 153.679   3316
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 13.46 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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:  1.66 (0.24), residues: 1282
  helix:  2.32 (0.20), residues: 708
  sheet:  0.09 (0.47), residues: 124
  loop : -0.59 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 270 
 HIS   0.005   0.001   HIS A 206 
 PHE   0.016   0.001   PHE A 163 
 TYR   0.017   0.001   TYR C 108 
 ARG   0.004   0.000   ARG A 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03741 (  640)
  hydrogen bonds       : angle       3.80697 ( 1760)
  covalent geometry    : bond        0.00498 (13247)
  covalent geometry    : angle       0.58561 (18518)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 56
  time to evaluate  : 1.163 
Fit side-chains
REVERT: A  166 MET cc_start: 0.8625 (tmm) cc_final: 0.8173 (tmm)
REVERT: D   93 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7276 (tm-30)
REVERT: C   30 CYS cc_start: 0.8827 (t) cc_final: 0.8493 (t)
REVERT: C  177 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.7683 (p0)
REVERT: F  160 LEU cc_start: 0.9691 (OUTLIER) cc_final: 0.9407 (mm)
REVERT: F  248 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8989 (mpp)
REVERT: F  273 CYS cc_start: 0.8246 (p) cc_final: 0.7673 (m)
  outliers start: 26
  outliers final: 20
  residues processed: 76
  average time/residue: 0.2031
  time to fit residues: 25.5127
Evaluate side-chains
  78 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 55
  time to evaluate  : 1.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 ILE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain D residue   23 PHE
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   64 ASN
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  177 ASP
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  249 HIS
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue  160 LEU
Chi-restraints excluded: chain F residue  243 ASP
Chi-restraints excluded: chain F residue  248 MET
Chi-restraints excluded: chain F residue  514 HIS
Chi-restraints excluded: chain F residue  637 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 89 optimal weight:   40.0000
   chunk 132 optimal weight:    7.9990
   chunk 126 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 87 optimal weight:   40.0000
   chunk 60 optimal weight:    2.9990
   chunk 98 optimal weight:   20.0000
   chunk 63 optimal weight:   10.0000
   chunk 72 optimal weight:    5.9990
   chunk 90 optimal weight:    7.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.059239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.042247 restraints weight = 56239.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.043948 restraints weight = 25999.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.045008 restraints weight = 16919.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.2499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  13247  Z= 0.211
  Angle     :  0.579  11.501  18518  Z= 0.297
  Chirality :  0.038   0.249   2230
  Planarity :  0.004   0.050   1937
  Dihedral  : 18.375 144.597   3316
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.75 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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:  1.62 (0.24), residues: 1282
  helix:  2.29 (0.20), residues: 707
  sheet:  0.04 (0.47), residues: 124
  loop : -0.61 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 270 
 HIS   0.014   0.001   HIS F 470 
 PHE   0.013   0.001   PHE A 163 
 TYR   0.013   0.001   TYR C 108 
 ARG   0.003   0.000   ARG A 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03728 (  640)
  hydrogen bonds       : angle       3.82094 ( 1760)
  covalent geometry    : bond        0.00450 (13247)
  covalent geometry    : angle       0.57932 (18518)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 57
  time to evaluate  : 1.279 
Fit side-chains
REVERT: A  166 MET cc_start: 0.8623 (tmm) cc_final: 0.8179 (tmm)
REVERT: C   30 CYS cc_start: 0.8834 (t) cc_final: 0.8464 (t)
REVERT: F  160 LEU cc_start: 0.9684 (OUTLIER) cc_final: 0.9400 (mm)
REVERT: F  273 CYS cc_start: 0.8196 (p) cc_final: 0.7633 (m)
  outliers start: 25
  outliers final: 23
  residues processed: 77
  average time/residue: 0.1966
  time to fit residues: 25.1697
Evaluate side-chains
  80 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 56
  time to evaluate  : 1.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 ILE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   23 PHE
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   64 ASN
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  188 THR
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  249 HIS
Chi-restraints excluded: chain C residue  268 LEU
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue  160 LEU
Chi-restraints excluded: chain F residue  243 ASP
Chi-restraints excluded: chain F residue  514 HIS
Chi-restraints excluded: chain F residue  637 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 89 optimal weight:   40.0000
   chunk 25 optimal weight:    1.9990
   chunk 92 optimal weight:   20.0000
   chunk 5 optimal weight:    0.8980
   chunk 138 optimal weight:    5.9990
   chunk 81 optimal weight:   10.0000
   chunk 120 optimal weight:   10.0000
   chunk 93 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 49 optimal weight:    8.9990
   chunk 105 optimal weight:   20.0000
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.059208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.042219 restraints weight = 56194.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.043899 restraints weight = 25978.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.044961 restraints weight = 17003.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  13247  Z= 0.212
  Angle     :  0.588  12.175  18518  Z= 0.301
  Chirality :  0.038   0.232   2230
  Planarity :  0.004   0.050   1937
  Dihedral  : 18.355 132.223   3316
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.94 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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:  1.62 (0.24), residues: 1282
  helix:  2.30 (0.20), residues: 707
  sheet:  0.01 (0.46), residues: 124
  loop : -0.61 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 270 
 HIS   0.015   0.001   HIS F 470 
 PHE   0.013   0.001   PHE A 163 
 TYR   0.012   0.001   TYR C 108 
 ARG   0.003   0.000   ARG A 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03763 (  640)
  hydrogen bonds       : angle       3.83219 ( 1760)
  covalent geometry    : bond        0.00453 (13247)
  covalent geometry    : angle       0.58840 (18518)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 57
  time to evaluate  : 1.343 
Fit side-chains
REVERT: A  166 MET cc_start: 0.8626 (tmm) cc_final: 0.8182 (tmm)
REVERT: C   30 CYS cc_start: 0.8817 (t) cc_final: 0.8437 (t)
REVERT: F  273 CYS cc_start: 0.8253 (p) cc_final: 0.7672 (m)
  outliers start: 25
  outliers final: 23
  residues processed: 78
  average time/residue: 0.1812
  time to fit residues: 23.5831
Evaluate side-chains
  79 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 56
  time to evaluate  : 1.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 ILE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   72 ASP
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain D residue   13 VAL
Chi-restraints excluded: chain D residue   23 PHE
Chi-restraints excluded: chain D residue   46 VAL
Chi-restraints excluded: chain D residue   79 VAL
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue   64 ASN
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  188 THR
Chi-restraints excluded: chain C residue  241 LEU
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  249 HIS
Chi-restraints excluded: chain C residue  268 LEU
Chi-restraints excluded: chain F residue   77 VAL
Chi-restraints excluded: chain F residue  243 ASP
Chi-restraints excluded: chain F residue  514 HIS
Chi-restraints excluded: chain F residue  637 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 121 optimal weight:    3.9990
   chunk 118 optimal weight:    0.0060
   chunk 13 optimal weight:    0.9980
   chunk 69 optimal weight:    7.9990
   chunk 104 optimal weight:    9.9990
   chunk 21 optimal weight:    6.9990
   chunk 59 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 107 optimal weight:    7.9990
   chunk 86 optimal weight:   10.0000
   overall best weight:    2.2002

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

Flipped N/Q/H residues before XYZ refinement:
** D  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.059638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.042711 restraints weight = 56182.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.044420 restraints weight = 25632.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.045456 restraints weight = 16627.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.2553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13247  Z= 0.162
  Angle     :  0.566  12.427  18518  Z= 0.289
  Chirality :  0.037   0.225   2230
  Planarity :  0.004   0.050   1937
  Dihedral  : 18.383 131.785   3316
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.13 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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:  1.66 (0.24), residues: 1282
  helix:  2.33 (0.20), residues: 708
  sheet:  0.04 (0.46), residues: 124
  loop : -0.59 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 270 
 HIS   0.010   0.001   HIS F 470 
 PHE   0.010   0.001   PHE A 163 
 TYR   0.011   0.001   TYR F 232 
 ARG   0.003   0.000   ARG A 182 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03546 (  640)
  hydrogen bonds       : angle       3.74542 ( 1760)
  covalent geometry    : bond        0.00350 (13247)
  covalent geometry    : angle       0.56561 (18518)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3663.66 seconds
wall clock time: 65 minutes 14.67 seconds (3914.67 seconds total)