Starting phenix.real_space_refine
on Wed Jul 30 15:28:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qp5_18543/07_2025/8qp5_18543.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qp5_18543/07_2025/8qp5_18543.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qp5_18543/07_2025/8qp5_18543.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qp5_18543/07_2025/8qp5_18543.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qp5_18543/07_2025/8qp5_18543.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qp5_18543/07_2025/8qp5_18543.cif"
  }
  resolution = 4.4
  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=   0.003 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      33      5.16       5
     C    7836      2.51       5
     N    2209      2.21       5
     O    2476      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 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: 12554
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4886
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 614, 4886
          Classifications: {'peptide': 614}
          Link IDs: {'PTRANS': 24, 'TRANS': 589}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "B"
      Number of atoms: 2674
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 357, 2674
          Classifications: {'peptide': 357}
          Link IDs: {'PTRANS': 11, 'TRANS': 345}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "C"
      Number of atoms: 1036
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 1036
          Classifications: {'peptide': 171}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 71}
          Link IDs: {'PTRANS': 10, 'TRANS': 160}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 280
          Unresolved non-hydrogen angles: 366
          Unresolved non-hydrogen dihedrals: 229
          Unresolved non-hydrogen chiralities: 25
          Planarities with less than four sites: {'GLN:plan1': 12, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 183
    Chain: "D"
      Number of atoms: 1744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1744
          Classifications: {'peptide': 216}
          Link IDs: {'PTRANS': 11, 'TRANS': 204}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "E"
      Number of atoms: 693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 693
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 5, 'TRANS': 83}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "P"
      Number of atoms: 1521
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 299, 1516
          Classifications: {'peptide': 299}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 217}
          Link IDs: {'PTRANS': 2, 'TRANS': 296}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 844
          Unresolved non-hydrogen angles: 1088
          Unresolved non-hydrogen dihedrals: 721
          Unresolved non-hydrogen chiralities: 65
          Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 8, 'TYR:plan': 14, 'ASN:plan1': 12, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 13, 'GLU:plan': 15, 'ARG:plan': 12}
          Unresolved non-hydrogen planarities: 509
      Conformer: "B"
        Number of residues, atoms: 299, 1516
          Classifications: {'peptide': 299}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 217}
          Link IDs: {'PTRANS': 2, 'TRANS': 296}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 844
          Unresolved non-hydrogen angles: 1088
          Unresolved non-hydrogen dihedrals: 721
          Unresolved non-hydrogen chiralities: 65
          Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 8, 'TYR:plan': 14, 'ASN:plan1': 12, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 13, 'GLU:plan': 15, 'ARG:plan': 12}
          Unresolved non-hydrogen planarities: 509
          bond proxies already assigned to first conformer: 1513
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR P1150 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BTYR P1150 " occ=0.50
  Time building chain proxies: 8.46, per 1000 atoms: 0.67
  Number of scatterers: 12554
  At special positions: 0
  Unit cell: (135.42, 130.24, 128.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      33     16.00
     O    2476      8.00
     N    2209      7.00
     C    7836      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: 2.94
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3164

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 19 sheets defined
      22.7% alpha, 29.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 189 through 196
      removed outlier: 3.791A  pdb=" N   HIS A 196 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 232
    Processing helix  chain 'A' and resid 280 through 289
      removed outlier: 3.556A  pdb=" N   ILE A 284 " --> pdb=" O   HIS A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 315
      removed outlier: 3.547A  pdb=" N   TYR A 315 " --> pdb=" O   LEU A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 332
      No H-bonds generated for 'chain 'A' and resid 330 through 332'
    Processing helix  chain 'A' and resid 361 through 367
      removed outlier: 3.809A  pdb=" N   LEU A 365 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 393
      removed outlier: 4.180A  pdb=" N   GLY A 393 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 501
      removed outlier: 3.605A  pdb=" N   ASP A 500 " --> pdb=" O   ASP A 497 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   LEU A 501 " --> pdb=" O   ASP A 498 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 497 through 501'
    Processing helix  chain 'A' and resid 542 through 553
    Processing helix  chain 'A' and resid 647 through 651
    Processing helix  chain 'A' and resid 729 through 731
      No H-bonds generated for 'chain 'A' and resid 729 through 731'
    Processing helix  chain 'B' and resid 136 through 139
    Processing helix  chain 'C' and resid 39 through 44
    Processing helix  chain 'C' and resid 76 through 80
      removed outlier: 3.574A  pdb=" N   LEU C  80 " --> pdb=" O   GLY C  77 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 114
      No H-bonds generated for 'chain 'C' and resid 112 through 114'
    Processing helix  chain 'C' and resid 115 through 125
    Processing helix  chain 'C' and resid 191 through 209
      removed outlier: 3.680A  pdb=" N   LEU C 209 " --> pdb=" O   ILE C 205 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 31 through 46
      removed outlier: 4.241A  pdb=" N   ILE D  35 " --> pdb=" O   PRO D  31 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 62
    Processing helix  chain 'D' and resid 67 through 82
      removed outlier: 3.758A  pdb=" N   VAL D  71 " --> pdb=" O   TYR D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 84 through 99
    Processing helix  chain 'D' and resid 104 through 121
      removed outlier: 3.584A  pdb=" N   VAL D 108 " --> pdb=" O   ASN D 104 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 124 through 129
    Processing helix  chain 'D' and resid 137 through 154
    Processing helix  chain 'D' and resid 159 through 189
    Processing helix  chain 'D' and resid 192 through 205
    Processing helix  chain 'D' and resid 208 through 225
      removed outlier: 3.736A  pdb=" N   ARG D 212 " --> pdb=" O   THR D 208 " (cutoff:3.500A)
      Proline residue:  D 216  - end of helix
    Processing helix  chain 'D' and resid 228 through 243
      removed outlier: 3.990A  pdb=" N   LYS D 233 " --> pdb=" O   ALA D 229 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   SER D 243 " --> pdb=" O   ALA D 239 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 39 through 45
    Processing helix  chain 'E' and resid 51 through 60
    Processing helix  chain 'P' and resid 1003 through 1022
      removed outlier: 3.562A  pdb=" N   ALA P1008 " --> pdb=" O   THR P1004 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 1024 through 1029
      removed outlier: 3.759A  pdb=" N   MET P1029 " --> pdb=" O   LEU P1025 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 1136 through 1139
      removed outlier: 3.693A  pdb=" N   LEU P1139 " --> pdb=" O   PHE P1136 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'P' and resid 1136 through 1139'
    Processing helix  chain 'P' and resid 1185 through 1189
    Processing helix  chain 'P' and resid 1282 through 1287
      removed outlier: 3.853A  pdb=" N   TYR P1286 " --> pdb=" O   ALA P1282 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 181
      removed outlier: 7.414A  pdb=" N   VAL A 256 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ILE A 180 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   VAL A 258 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   THR A 261 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   ILE A 240 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 274
      removed outlier: 7.198A  pdb=" N   LEU A 337 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   VAL A 271 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   VAL A 339 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   VAL A 273 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 7.469A  pdb=" N   VAL A 341 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 349 through 355
      removed outlier: 4.057A  pdb=" N   VAL A 349 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 7.596A  pdb=" N   VAL A 414 " --> pdb=" O   VAL A 349 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   LYS A 351 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 8.235A  pdb=" N   TYR A 416 " --> pdb=" O   LYS A 351 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   ARG A 353 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 7.731A  pdb=" N   VAL A 418 " --> pdb=" O   ARG A 353 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   GLU A 355 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   GLU A 420 " --> pdb=" O   GLU A 355 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   THR A 397 " --> pdb=" O   LYS A 419 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 781 through 783
      removed outlier: 6.267A  pdb=" N   ALA A 770 " --> pdb=" O   PRO A 790 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   ILE A 772 " --> pdb=" O   ALA A 788 " (cutoff:3.500A)
      removed outlier: 5.011A  pdb=" N   ALA A 788 " --> pdb=" O   ILE A 772 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   LEU A 774 " --> pdb=" O   SER A 786 " (cutoff:3.500A)
      removed outlier: 5.678A  pdb=" N   SER A 786 " --> pdb=" O   LEU A 774 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 781 through 783
      removed outlier: 3.571A  pdb=" N   GLY A 742 " --> pdb=" O   ARG A 767 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   THR A 467 " --> pdb=" O   ASP A 493 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 671 through 674
      removed outlier: 4.549A  pdb=" N   ALA A 672 " --> pdb=" O   SER A 702 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 45 through 49
      removed outlier: 3.633A  pdb=" N   THR B  45 " --> pdb=" O   THR B 391 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   SER B 389 " --> pdb=" O   ALA B  47 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   LEU B 378 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 68
      removed outlier: 3.747A  pdb=" N   ALA B  66 " --> pdb=" O   TYR B  73 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   VAL B  81 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   SER B  94 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ALA B  83 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 118
      removed outlier: 3.682A  pdb=" N   THR B 116 " --> pdb=" O   TYR B 123 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 156 through 158
      removed outlier: 3.664A  pdb=" N   VAL B 156 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   TRP B 183 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 201 through 203
      removed outlier: 3.794A  pdb=" N   TRP B 228 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   LEU B 220 " --> pdb=" O   MET B 226 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   MET B 226 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 253 through 254
      removed outlier: 3.798A  pdb=" N   ALA B 260 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   THR B 268 " --> pdb=" O   ALA B 260 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   ALA B 262 " --> pdb=" O   ASN B 266 " (cutoff:3.500A)
      removed outlier: 5.218A  pdb=" N   ASN B 266 " --> pdb=" O   ALA B 262 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   TRP B 279 " --> pdb=" O   ALA B 269 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   ASP B 271 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ILE B 277 " --> pdb=" O   ASP B 271 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 295 through 299
      removed outlier: 3.661A  pdb=" N   LEU B 298 " --> pdb=" O   MET B 306 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   MET B 306 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 331 through 333
    Processing sheet with id=AB6, first strand: chain 'C' and resid 134 through 136
      removed outlier: 3.741A  pdb=" N   ASP C 136 " --> pdb=" O   LEU C 141 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 33
      removed outlier: 4.667A  pdb=" N   MET E  64 " --> pdb=" O   PHE E  74 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 33
    Processing sheet with id=AB9, first strand: chain 'P' and resid 1040 through 1051
      removed outlier: 3.646A  pdb=" N   VAL P1103 " --> pdb=" O   HIS P1127 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ASP P1209 " --> pdb=" O   GLU P1168 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'P' and resid 1182 through 1183

    625 hydrogen bonds defined for protein.
    1726 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.53

  Time building geometry restraints manager: 3.52 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: 3877
        1.33 -     1.45: 1956
        1.45 -     1.57: 6897
        1.57 -     1.69: 0
        1.69 -     1.81: 63
  Bond restraints: 12793
  Sorted by residual:
  bond pdb=" N   ILE C 131 "
       pdb=" CA  ILE C 131 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.24e-02 6.50e+03 8.19e+00
  bond pdb=" N   ASN C 110 "
       pdb=" CA  ASN C 110 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.034 1.18e-02 7.18e+03 8.10e+00
  bond pdb=" N   LEU C 106 "
       pdb=" CA  LEU C 106 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.23e-02 6.61e+03 6.60e+00
  bond pdb=" N   SER C 105 "
       pdb=" CA  SER C 105 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.34e-02 5.57e+03 6.47e+00
  bond pdb=" N   LYS C 127 "
       pdb=" CA  LYS C 127 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.20e-02 6.94e+03 5.79e+00
  ... (remaining 12788 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 17159
        2.10 -     4.21: 258
        4.21 -     6.31: 17
        6.31 -     8.42: 3
        8.42 -    10.52: 3
  Bond angle restraints: 17440
  Sorted by residual:
  angle pdb=" C   THR A 479 "
        pdb=" N   VAL A 480 "
        pdb=" CA  VAL A 480 "
      ideal   model   delta    sigma   weight residual
     121.65  117.82    3.83 9.40e-01 1.13e+00 1.66e+01
  angle pdb=" N   LEU C 124 "
        pdb=" CA  LEU C 124 "
        pdb=" C   LEU C 124 "
      ideal   model   delta    sigma   weight residual
     113.01  108.67    4.34 1.20e+00 6.94e-01 1.31e+01
  angle pdb=" CB  MET D 227 "
        pdb=" CG  MET D 227 "
        pdb=" SD  MET D 227 "
      ideal   model   delta    sigma   weight residual
     112.70  123.10  -10.40 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" N   ASN C 128 "
        pdb=" CA  ASN C 128 "
        pdb=" C   ASN C 128 "
      ideal   model   delta    sigma   weight residual
     114.39  109.39    5.00 1.45e+00 4.76e-01 1.19e+01
  angle pdb=" CA  SER C 105 "
        pdb=" C   SER C 105 "
        pdb=" O   SER C 105 "
      ideal   model   delta    sigma   weight residual
     121.87  118.24    3.63 1.16e+00 7.43e-01 9.77e+00
  ... (remaining 17435 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 6855
       17.73 -    35.46: 542
       35.46 -    53.19: 82
       53.19 -    70.92: 18
       70.92 -    88.65: 4
  Dihedral angle restraints: 7501
    sinusoidal: 2526
      harmonic: 4975
  Sorted by residual:
  dihedral pdb=" CA  VAL A 480 "
           pdb=" C   VAL A 480 "
           pdb=" N   ASP A 481 "
           pdb=" CA  ASP A 481 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.18   19.82     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  GLU A 717 "
           pdb=" C   GLU A 717 "
           pdb=" N   PHE A 718 "
           pdb=" CA  PHE A 718 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.24   19.76     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  ASN A 259 "
           pdb=" C   ASN A 259 "
           pdb=" N   ILE A 260 "
           pdb=" CA  ILE A 260 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.80  -18.20     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 7498 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1336
       0.040 -    0.080: 444
       0.080 -    0.119: 151
       0.119 -    0.159: 15
       0.159 -    0.199: 5
  Chirality restraints: 1951
  Sorted by residual:
  chirality pdb=" CG  LEU D 167 "
            pdb=" CB  LEU D 167 "
            pdb=" CD1 LEU D 167 "
            pdb=" CD2 LEU D 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 9.91e-01
  chirality pdb=" CA  PHE A 586 "
            pdb=" N   PHE A 586 "
            pdb=" C   PHE A 586 "
            pdb=" CB  PHE A 586 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.70e-01
  chirality pdb=" CA  ILE C 131 "
            pdb=" N   ILE C 131 "
            pdb=" C   ILE C 131 "
            pdb=" CB  ILE C 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.98e-01
  ... (remaining 1948 not shown)

  Planarity restraints: 2338
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 492 "    0.012 2.00e-02 2.50e+03   2.36e-02 5.58e+00
        pdb=" C   ASN A 492 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   ASN A 492 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ASP A 493 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 586 "   -0.017 2.00e-02 2.50e+03   1.39e-02 3.36e+00
        pdb=" CG  PHE A 586 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 586 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 586 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 586 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 586 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 586 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 136 "    0.025 5.00e-02 4.00e+02   3.84e-02 2.36e+00
        pdb=" N   PRO D 137 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO D 137 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 137 "    0.021 5.00e-02 4.00e+02
  ... (remaining 2335 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 292
        2.67 -     3.23: 12474
        3.23 -     3.79: 19221
        3.79 -     4.34: 24775
        4.34 -     4.90: 40392
  Nonbonded interactions: 97154
  Sorted by model distance:
  nonbonded pdb=" O   GLY E  60 "
            pdb=" OH  TYR E  75 "
     model   vdw
     2.113 3.040
  nonbonded pdb=" O   ILE D 238 "
            pdb=" OG  SER D 242 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" OH  TYR A 608 "
            pdb=" OE1 GLU A 650 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OD1 ASN A 297 "
            pdb=" OG1 THR A 299 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" OG1 THR E  39 "
            pdb=" OD1 ASN E  41 "
     model   vdw
     2.196 3.040
  ... (remaining 97149 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=0.50 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:             1.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.570
  Check model and map are aligned:         0.100
  Set scattering table:                    0.110
  Process input model:                     32.410
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
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      :  0.003   0.035  12793  Z= 0.174
  Angle     :  0.626  10.521  17440  Z= 0.346
  Chirality :  0.044   0.199   1951
  Planarity :  0.004   0.038   2338
  Dihedral  : 13.403  88.651   4337
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 15.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.69 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.20), residues: 1729
  helix:  1.26 (0.28), residues: 310
  sheet: -0.76 (0.21), residues: 570
  loop : -2.04 (0.21), residues: 849

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  93 
 HIS   0.004   0.001   HIS A 533 
 PHE   0.031   0.001   PHE A 586 
 TYR   0.020   0.001   TYR A 230 
 ARG   0.005   0.000   ARG D  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14475 (  619)
  hydrogen bonds       : angle       6.46554 ( 1726)
  covalent geometry    : bond        0.00324 (12793)
  covalent geometry    : angle       0.62586 (17440)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 193
  time to evaluate  : 1.520 
Fit side-chains
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
REVERT: A  191 ASP cc_start: 0.9102 (p0) cc_final: 0.8773 (p0)
REVERT: B   93 TRP cc_start: 0.4473 (p-90) cc_final: 0.4225 (p-90)
REVERT: B  123 TYR cc_start: 0.7907 (m-80) cc_final: 0.7540 (m-80)
REVERT: B  347 HIS cc_start: 0.7976 (m-70) cc_final: 0.7694 (m-70)
REVERT: D   74 ASP cc_start: 0.9310 (m-30) cc_final: 0.9068 (m-30)
REVERT: D  105 ILE cc_start: 0.9123 (mm) cc_final: 0.8822 (mm)
REVERT: D  232 GLU cc_start: 0.9130 (mp0) cc_final: 0.8887 (mp0)
REVERT: E   28 TYR cc_start: 0.8906 (t80) cc_final: 0.8254 (t80)
  outliers start: 2
  outliers final: 1
  residues processed: 195
  average time/residue: 0.2298
  time to fit residues: 67.3494
Evaluate side-chains
  155 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 154
  time to evaluate  : 1.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 144 optimal weight:    0.0030
   chunk 129 optimal weight:    5.9990
   chunk 71 optimal weight:   10.0000
   chunk 44 optimal weight:    0.7980
   chunk 87 optimal weight:   20.0000
   chunk 69 optimal weight:   20.0000
   chunk 134 optimal weight:    8.9990
   chunk 51 optimal weight:   10.0000
   chunk 81 optimal weight:    8.9990
   chunk 99 optimal weight:    3.9990
   chunk 155 optimal weight:   50.0000
   overall best weight:    3.9596

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

Flipped N/Q/H residues before XYZ refinement:
A 244 GLN
B 168 ASN
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  54 GLN ** 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 = 0.3654 r_free = 0.3654 target = 0.100613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.066353 restraints weight = 44421.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.067644 restraints weight = 28083.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.067608 restraints weight = 17822.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2917
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2917 r_free = 0.2917    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2917 r_free = 0.2917    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2917
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.1086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  12793  Z= 0.206
  Angle     :  0.602   8.994  17440  Z= 0.328
  Chirality :  0.044   0.182   1951
  Planarity :  0.004   0.043   2338
  Dihedral  :  4.745  23.386   1878
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  7.45 %
    Favored  : 92.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.20), residues: 1729
  helix:  0.71 (0.26), residues: 325
  sheet: -0.88 (0.21), residues: 582
  loop : -2.09 (0.21), residues: 822

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 143 
 HIS   0.004   0.001   HIS A 533 
 PHE   0.031   0.002   PHE A 586 
 TYR   0.018   0.002   TYR A 754 
 ARG   0.005   0.001   ARG A 366 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04177 (  619)
  hydrogen bonds       : angle       5.74850 ( 1726)
  covalent geometry    : bond        0.00451 (12793)
  covalent geometry    : angle       0.60225 (17440)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 195
  time to evaluate  : 1.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
REVERT: A  193 LEU cc_start: 0.9207 (mt) cc_final: 0.8962 (mt)
REVERT: A  321 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.7807 (mtm-85)
REVERT: B  111 LEU cc_start: 0.9074 (mp) cc_final: 0.8851 (mp)
REVERT: B  123 TYR cc_start: 0.7938 (m-80) cc_final: 0.7465 (m-80)
REVERT: B  346 LEU cc_start: 0.8429 (mp) cc_final: 0.7828 (tt)
REVERT: C   78 LYS cc_start: 0.8513 (mttp) cc_final: 0.8215 (mttm)
REVERT: D   74 ASP cc_start: 0.9349 (m-30) cc_final: 0.9074 (m-30)
REVERT: D  105 ILE cc_start: 0.9284 (mm) cc_final: 0.8964 (mm)
REVERT: D  109 MET cc_start: 0.8862 (mtp) cc_final: 0.8481 (mtp)
REVERT: D  219 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8140 (tm-30)
REVERT: D  232 GLU cc_start: 0.9022 (mp0) cc_final: 0.8748 (mp0)
REVERT: E   50 MET cc_start: 0.8100 (ptp) cc_final: 0.7773 (ptp)
REVERT: P 1271 ASN cc_start: 0.7943 (t0) cc_final: 0.7328 (t0)
  outliers start: 2
  outliers final: 2
  residues processed: 196
  average time/residue: 0.2442
  time to fit residues: 72.2905
Evaluate side-chains
  162 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 160
  time to evaluate  : 1.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 10 optimal weight:   20.0000
   chunk 63 optimal weight:   20.0000
   chunk 43 optimal weight:    8.9990
   chunk 155 optimal weight:   50.0000
   chunk 134 optimal weight:    8.9990
   chunk 141 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9980
   chunk 159 optimal weight:    0.6980
   chunk 55 optimal weight:    3.9990
   chunk 114 optimal weight:    9.9990
   overall best weight:    4.5386

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

Flipped N/Q/H residues before XYZ refinement:
B 172 GLN
** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 GLN
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  54 GLN ** 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 = 0.3642 r_free = 0.3642 target = 0.100015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.065166 restraints weight = 45398.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.067659 restraints weight = 27556.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.067569 restraints weight = 16922.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2896
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2896
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.1464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  12793  Z= 0.229
  Angle     :  0.626   8.203  17440  Z= 0.340
  Chirality :  0.044   0.171   1951
  Planarity :  0.005   0.100   2338
  Dihedral  :  4.879  23.543   1878
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  5.72 %
    Favored  : 94.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.20), residues: 1729
  helix:  0.59 (0.27), residues: 325
  sheet: -0.92 (0.21), residues: 576
  loop : -2.18 (0.21), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 143 
 HIS   0.003   0.001   HIS A 533 
 PHE   0.024   0.002   PHE A 586 
 TYR   0.024   0.002   TYR B 132 
 ARG   0.007   0.001   ARG C 196 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04260 (  619)
  hydrogen bonds       : angle       5.75984 ( 1726)
  covalent geometry    : bond        0.00500 (12793)
  covalent geometry    : angle       0.62625 (17440)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 200
  time to evaluate  : 1.545 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
REVERT: A  193 LEU cc_start: 0.9283 (mt) cc_final: 0.9017 (mt)
REVERT: A  369 MET cc_start: 0.9090 (mmt) cc_final: 0.8770 (mmt)
REVERT: B   93 TRP cc_start: 0.4491 (p-90) cc_final: 0.4140 (p-90)
REVERT: B  111 LEU cc_start: 0.9113 (mp) cc_final: 0.8884 (mp)
REVERT: B  123 TYR cc_start: 0.8022 (m-80) cc_final: 0.7456 (m-80)
REVERT: B  132 TYR cc_start: 0.8442 (m-80) cc_final: 0.8235 (m-80)
REVERT: B  347 HIS cc_start: 0.8087 (m90) cc_final: 0.7754 (m-70)
REVERT: D   74 ASP cc_start: 0.9274 (m-30) cc_final: 0.9026 (m-30)
REVERT: D  109 MET cc_start: 0.9004 (mtp) cc_final: 0.8655 (mtp)
REVERT: E   50 MET cc_start: 0.7705 (ptp) cc_final: 0.7281 (ptp)
REVERT: P 1271 ASN cc_start: 0.7921 (t0) cc_final: 0.7203 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 201
  average time/residue: 0.2576
  time to fit residues: 76.1201
Evaluate side-chains
  159 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 158
  time to evaluate  : 1.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 42 optimal weight:    9.9990
   chunk 87 optimal weight:    2.9990
   chunk 60 optimal weight:   10.0000
   chunk 93 optimal weight:    7.9990
   chunk 118 optimal weight:    2.9990
   chunk 160 optimal weight:   50.0000
   chunk 86 optimal weight:    4.9990
   chunk 124 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0060
   chunk 148 optimal weight:    8.9990
   chunk 126 optimal weight:    1.9990
   overall best weight:    2.4004

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

Flipped N/Q/H residues before XYZ refinement:
** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 GLN
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  54 GLN ** 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 = 0.3679 r_free = 0.3679 target = 0.102049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.069279 restraints weight = 43759.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.070331 restraints weight = 25860.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.069968 restraints weight = 18221.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2964
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2964 r_free = 0.2964    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2964 r_free = 0.2964    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2964
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.1531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12793  Z= 0.143
  Angle     :  0.577   9.509  17440  Z= 0.309
  Chirality :  0.043   0.185   1951
  Planarity :  0.004   0.051   2338
  Dihedral  :  4.652  21.721   1878
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.64 %
    Favored  : 96.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.61 (0.20), residues: 1729
  helix:  0.99 (0.27), residues: 322
  sheet: -0.85 (0.21), residues: 579
  loop : -2.08 (0.21), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 143 
 HIS   0.002   0.001   HIS A 533 
 PHE   0.026   0.001   PHE A 586 
 TYR   0.022   0.001   TYR D  67 
 ARG   0.005   0.000   ARG C 196 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03754 (  619)
  hydrogen bonds       : angle       5.43890 ( 1726)
  covalent geometry    : bond        0.00312 (12793)
  covalent geometry    : angle       0.57703 (17440)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 208
  time to evaluate  : 1.497 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
REVERT: A  193 LEU cc_start: 0.9202 (mt) cc_final: 0.8985 (mt)
REVERT: A  369 MET cc_start: 0.9114 (mmt) cc_final: 0.8838 (mmt)
REVERT: A  646 MET cc_start: 0.8420 (ptp) cc_final: 0.8110 (ptp)
REVERT: B   93 TRP cc_start: 0.4605 (p-90) cc_final: 0.4269 (p-90)
REVERT: B  111 LEU cc_start: 0.9086 (mp) cc_final: 0.8867 (mp)
REVERT: B  123 TYR cc_start: 0.7928 (m-80) cc_final: 0.7349 (m-80)
REVERT: B  132 TYR cc_start: 0.8275 (m-80) cc_final: 0.8017 (m-80)
REVERT: B  346 LEU cc_start: 0.8456 (mp) cc_final: 0.7857 (tt)
REVERT: B  347 HIS cc_start: 0.8104 (m90) cc_final: 0.7875 (m-70)
REVERT: C  195 GLN cc_start: 0.7390 (pp30) cc_final: 0.6905 (pp30)
REVERT: D   74 ASP cc_start: 0.9230 (m-30) cc_final: 0.8980 (m-30)
REVERT: D  109 MET cc_start: 0.9010 (mtp) cc_final: 0.8697 (mtp)
REVERT: D  219 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8136 (tm-30)
REVERT: D  232 GLU cc_start: 0.9035 (mp0) cc_final: 0.8803 (mp0)
REVERT: P 1271 ASN cc_start: 0.7895 (t0) cc_final: 0.7291 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 209
  average time/residue: 0.2305
  time to fit residues: 71.3564
Evaluate side-chains
  165 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 164
  time to evaluate  : 1.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 43 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   chunk 97 optimal weight:    5.9990
   chunk 104 optimal weight:    6.9990
   chunk 100 optimal weight:    4.9990
   chunk 118 optimal weight:    4.9990
   chunk 116 optimal weight:    5.9990
   chunk 161 optimal weight:   20.0000
   chunk 72 optimal weight:    6.9990
   chunk 88 optimal weight:   20.0000
   chunk 151 optimal weight:   40.0000
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 HIS
** E  34 GLN ** 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 = 0.3647 r_free = 0.3647 target = 0.100289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.064631 restraints weight = 44896.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.066820 restraints weight = 27901.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.067325 restraints weight = 19322.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2896
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2896
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.1886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  12793  Z= 0.249
  Angle     :  0.648   9.781  17440  Z= 0.351
  Chirality :  0.045   0.171   1951
  Planarity :  0.005   0.043   2338
  Dihedral  :  5.009  24.747   1878
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.97 %
    Favored  : 90.03 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  4.68 %
    Favored  : 95.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.89 (0.20), residues: 1729
  helix:  0.54 (0.27), residues: 324
  sheet: -0.98 (0.21), residues: 588
  loop : -2.22 (0.21), residues: 817

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 576 
 HIS   0.003   0.001   HIS A 196 
 PHE   0.029   0.002   PHE A 586 
 TYR   0.019   0.002   TYR D  67 
 ARG   0.007   0.001   ARG A 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04299 (  619)
  hydrogen bonds       : angle       5.79737 ( 1726)
  covalent geometry    : bond        0.00544 (12793)
  covalent geometry    : angle       0.64799 (17440)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 200
  time to evaluate  : 1.524 
Fit side-chains
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
REVERT: A  193 LEU cc_start: 0.9226 (mt) cc_final: 0.9025 (mt)
REVERT: A  321 ARG cc_start: 0.7943 (mtm110) cc_final: 0.7659 (mtm-85)
REVERT: A  369 MET cc_start: 0.9350 (mmt) cc_final: 0.8834 (mmt)
REVERT: A  650 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8840 (mt-10)
REVERT: B  111 LEU cc_start: 0.9095 (mp) cc_final: 0.8766 (mp)
REVERT: B  123 TYR cc_start: 0.7991 (m-80) cc_final: 0.7303 (m-80)
REVERT: B  221 MET cc_start: 0.8002 (ptm) cc_final: 0.7706 (ppp)
REVERT: B  347 HIS cc_start: 0.8078 (m90) cc_final: 0.7719 (m-70)
REVERT: C  195 GLN cc_start: 0.7394 (pp30) cc_final: 0.6902 (pp30)
REVERT: D   54 GLN cc_start: 0.8636 (tt0) cc_final: 0.8383 (tt0)
REVERT: D   74 ASP cc_start: 0.9278 (m-30) cc_final: 0.9026 (m-30)
REVERT: D  219 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8159 (tm-30)
REVERT: P 1271 ASN cc_start: 0.7962 (t0) cc_final: 0.7423 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 201
  average time/residue: 0.2304
  time to fit residues: 69.2483
Evaluate side-chains
  163 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 162
  time to evaluate  : 1.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 129 optimal weight:    0.9980
   chunk 43 optimal weight:    8.9990
   chunk 64 optimal weight:    5.9990
   chunk 90 optimal weight:    7.9990
   chunk 98 optimal weight:    0.0020
   chunk 126 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 84 optimal weight:    0.0970
   chunk 128 optimal weight:    0.9990
   chunk 114 optimal weight:    0.9980
   chunk 163 optimal weight:    0.0040
   overall best weight:    0.4198

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN
B 230 GLN
B 302 ASN
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.103890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.068761 restraints weight = 44759.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.070962 restraints weight = 24540.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.072417 restraints weight = 16532.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3032
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3032
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12793  Z= 0.106
  Angle     :  0.570   9.159  17440  Z= 0.300
  Chirality :  0.043   0.164   1951
  Planarity :  0.004   0.042   2338
  Dihedral  :  4.478  19.220   1878
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.12 %
    Favored  : 96.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.20), residues: 1729
  helix:  1.32 (0.28), residues: 317
  sheet: -0.74 (0.21), residues: 574
  loop : -2.04 (0.21), residues: 838

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 376 
 HIS   0.003   0.000   HIS D 139 
 PHE   0.024   0.001   PHE A 586 
 TYR   0.021   0.001   TYR D 184 
 ARG   0.004   0.000   ARG A 734 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03364 (  619)
  hydrogen bonds       : angle       5.14647 ( 1726)
  covalent geometry    : bond        0.00220 (12793)
  covalent geometry    : angle       0.57024 (17440)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 222
  time to evaluate  : 1.717 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
REVERT: A  369 MET cc_start: 0.9316 (mmt) cc_final: 0.8901 (mmt)
REVERT: A  768 MET cc_start: 0.6943 (ttt) cc_final: 0.6409 (tmm)
REVERT: B   93 TRP cc_start: 0.4519 (p-90) cc_final: 0.4200 (p-90)
REVERT: B  123 TYR cc_start: 0.7824 (m-80) cc_final: 0.7272 (m-80)
REVERT: B  182 LYS cc_start: 0.9160 (mmtp) cc_final: 0.8938 (mmtp)
REVERT: B  221 MET cc_start: 0.7805 (ptm) cc_final: 0.7338 (ppp)
REVERT: B  346 LEU cc_start: 0.8395 (mp) cc_final: 0.7861 (tt)
REVERT: C  195 GLN cc_start: 0.7440 (pp30) cc_final: 0.6925 (pp30)
REVERT: D   35 ILE cc_start: 0.7261 (pt) cc_final: 0.6940 (pt)
REVERT: D   74 ASP cc_start: 0.9241 (m-30) cc_final: 0.8951 (m-30)
REVERT: D  105 ILE cc_start: 0.9192 (mm) cc_final: 0.8666 (mm)
REVERT: D  109 MET cc_start: 0.8919 (mtp) cc_final: 0.8649 (mtp)
REVERT: D  219 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8127 (tm-30)
REVERT: D  236 LYS cc_start: 0.9263 (ptmt) cc_final: 0.8907 (ptmm)
REVERT: E   50 MET cc_start: 0.8205 (ptm) cc_final: 0.7862 (ptm)
REVERT: P 1271 ASN cc_start: 0.7754 (t0) cc_final: 0.7393 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 223
  average time/residue: 0.2270
  time to fit residues: 75.1055
Evaluate side-chains
  176 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 175
  time to evaluate  : 1.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 163 optimal weight:    2.9990
   chunk 142 optimal weight:   50.0000
   chunk 3 optimal weight:   10.0000
   chunk 39 optimal weight:    9.9990
   chunk 167 optimal weight:    6.9990
   chunk 97 optimal weight:    3.9990
   chunk 70 optimal weight:   10.0000
   chunk 143 optimal weight:    9.9990
   chunk 1 optimal weight:    9.9990
   chunk 144 optimal weight:    7.9990
   chunk 88 optimal weight:    0.0060
   overall best weight:    4.4004

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

Flipped N/Q/H residues before XYZ refinement:
** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  36 ASN
** E  54 GLN ** 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 = 0.3658 r_free = 0.3658 target = 0.100710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.067640 restraints weight = 44720.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.068581 restraints weight = 28847.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.068968 restraints weight = 19752.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2957
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2957
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  12793  Z= 0.226
  Angle     :  0.644   9.351  17440  Z= 0.346
  Chirality :  0.045   0.226   1951
  Planarity :  0.005   0.041   2338
  Dihedral  :  4.820  23.923   1878
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.86 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  1.91 %
    Favored  : 97.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.20), residues: 1729
  helix:  0.83 (0.27), residues: 321
  sheet: -0.96 (0.21), residues: 586
  loop : -2.14 (0.21), residues: 822

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 776 
 HIS   0.005   0.001   HIS D 139 
 PHE   0.021   0.002   PHE A 586 
 TYR   0.017   0.002   TYR A 468 
 ARG   0.004   0.001   ARG D  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04082 (  619)
  hydrogen bonds       : angle       5.55375 ( 1726)
  covalent geometry    : bond        0.00493 (12793)
  covalent geometry    : angle       0.64396 (17440)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 192
  time to evaluate  : 1.570 
Fit side-chains
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
REVERT: A  193 LEU cc_start: 0.9191 (mt) cc_final: 0.8988 (mt)
REVERT: A  321 ARG cc_start: 0.7895 (mtm110) cc_final: 0.7609 (mtm-85)
REVERT: A  427 ASN cc_start: 0.8403 (t0) cc_final: 0.8192 (t0)
REVERT: A  650 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8807 (pt0)
REVERT: A  717 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7899 (tt0)
REVERT: B   93 TRP cc_start: 0.4718 (p-90) cc_final: 0.4317 (p-90)
REVERT: B  123 TYR cc_start: 0.7888 (m-80) cc_final: 0.7247 (m-80)
REVERT: B  221 MET cc_start: 0.7883 (ptm) cc_final: 0.7537 (ppp)
REVERT: C  195 GLN cc_start: 0.7439 (pp30) cc_final: 0.6950 (pp30)
REVERT: D   74 ASP cc_start: 0.9220 (m-30) cc_final: 0.8959 (m-30)
REVERT: D  109 MET cc_start: 0.8897 (mtp) cc_final: 0.8614 (mtp)
REVERT: D  219 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8117 (tm-30)
REVERT: D  225 MET cc_start: 0.9020 (mmt) cc_final: 0.8778 (tpp)
REVERT: D  232 GLU cc_start: 0.9001 (mp0) cc_final: 0.8522 (mp0)
REVERT: E   50 MET cc_start: 0.8151 (ptm) cc_final: 0.7730 (ptm)
REVERT: P 1271 ASN cc_start: 0.8082 (t0) cc_final: 0.7583 (t0)
  outliers start: 2
  outliers final: 2
  residues processed: 194
  average time/residue: 0.2477
  time to fit residues: 73.6908
Evaluate side-chains
  161 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 159
  time to evaluate  : 1.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 156 optimal weight:   20.0000
   chunk 7 optimal weight:    6.9990
   chunk 158 optimal weight:   40.0000
   chunk 152 optimal weight:   40.0000
   chunk 47 optimal weight:    7.9990
   chunk 104 optimal weight:   10.0000
   chunk 97 optimal weight:    6.9990
   chunk 155 optimal weight:   20.0000
   chunk 76 optimal weight:    6.9990
   chunk 142 optimal weight:   50.0000
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  36 ASN
** E  54 GLN ** 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 = 0.3623 r_free = 0.3623 target = 0.098731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.064137 restraints weight = 45527.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.065939 restraints weight = 28616.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.066136 restraints weight = 18730.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2863
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2863 r_free = 0.2863    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2863 r_free = 0.2863    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2863
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.057  12793  Z= 0.348
  Angle     :  0.753   9.243  17440  Z= 0.410
  Chirality :  0.048   0.290   1951
  Planarity :  0.005   0.056   2338
  Dihedral  :  5.478  25.714   1878
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 15.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.14 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  2.43 %
    Favored  : 97.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.23 (0.19), residues: 1729
  helix:  0.17 (0.26), residues: 321
  sheet: -1.16 (0.21), residues: 575
  loop : -2.40 (0.20), residues: 833

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 776 
 HIS   0.004   0.001   HIS A 196 
 PHE   0.027   0.003   PHE P1296 
 TYR   0.024   0.003   TYR D  67 
 ARG   0.008   0.001   ARG A 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04741 (  619)
  hydrogen bonds       : angle       6.15653 ( 1726)
  covalent geometry    : bond        0.00755 (12793)
  covalent geometry    : angle       0.75350 (17440)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 183
  time to evaluate  : 1.501 
Fit side-chains
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
REVERT: A  193 LEU cc_start: 0.9271 (mt) cc_final: 0.9047 (mt)
REVERT: A  321 ARG cc_start: 0.7857 (mtm110) cc_final: 0.7617 (mtm-85)
REVERT: A  598 LYS cc_start: 0.8787 (tptt) cc_final: 0.8506 (tppt)
REVERT: A  717 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7971 (tt0)
REVERT: B  123 TYR cc_start: 0.7946 (m-80) cc_final: 0.7241 (m-80)
REVERT: B  221 MET cc_start: 0.7996 (ptm) cc_final: 0.7731 (ppp)
REVERT: B  347 HIS cc_start: 0.8037 (m90) cc_final: 0.7725 (m-70)
REVERT: C  195 GLN cc_start: 0.7441 (pp30) cc_final: 0.6971 (pp30)
REVERT: D   56 GLU cc_start: 0.9139 (pt0) cc_final: 0.8886 (pt0)
REVERT: D   74 ASP cc_start: 0.9273 (m-30) cc_final: 0.9003 (m-30)
REVERT: D  109 MET cc_start: 0.9004 (mtp) cc_final: 0.8794 (mtp)
REVERT: E   50 MET cc_start: 0.8149 (ptm) cc_final: 0.7703 (ptm)
REVERT: P 1271 ASN cc_start: 0.8146 (t0) cc_final: 0.7549 (t0)
  outliers start: 2
  outliers final: 2
  residues processed: 185
  average time/residue: 0.2864
  time to fit residues: 82.6807
Evaluate side-chains
  157 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 155
  time to evaluate  : 1.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 36 optimal weight:    9.9990
   chunk 80 optimal weight:    4.9990
   chunk 51 optimal weight:    5.9990
   chunk 144 optimal weight:   30.0000
   chunk 110 optimal weight:    2.9990
   chunk 118 optimal weight:    0.7980
   chunk 151 optimal weight:   50.0000
   chunk 135 optimal weight:    5.9990
   chunk 165 optimal weight:   50.0000
   chunk 13 optimal weight:    6.9990
   chunk 103 optimal weight:    6.9990
   overall best weight:    4.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  36 ASN
** E  54 GLN ** 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 = 0.3651 r_free = 0.3651 target = 0.100425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.066340 restraints weight = 44159.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.067428 restraints weight = 28558.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.067476 restraints weight = 18086.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2908
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2908
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.2291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070  12793  Z= 0.218
  Angle     :  0.665  11.777  17440  Z= 0.357
  Chirality :  0.046   0.209   1951
  Planarity :  0.005   0.048   2338
  Dihedral  :  5.203  23.852   1878
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.86 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  1.13 %
    Favored  : 98.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.17 (0.19), residues: 1729
  helix:  0.25 (0.27), residues: 329
  sheet: -1.15 (0.21), residues: 577
  loop : -2.37 (0.20), residues: 823

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 776 
 HIS   0.002   0.001   HIS A 196 
 PHE   0.026   0.002   PHE A 586 
 TYR   0.019   0.002   TYR D  67 
 ARG   0.012   0.001   ARG E  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04231 (  619)
  hydrogen bonds       : angle       5.77502 ( 1726)
  covalent geometry    : bond        0.00478 (12793)
  covalent geometry    : angle       0.66542 (17440)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 195
  time to evaluate  : 2.146 
Fit side-chains
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
REVERT: A  193 LEU cc_start: 0.9250 (mt) cc_final: 0.9039 (mt)
REVERT: A  321 ARG cc_start: 0.7881 (mtm110) cc_final: 0.7632 (mtm-85)
REVERT: A  598 LYS cc_start: 0.8792 (tptt) cc_final: 0.8559 (tppt)
REVERT: A  717 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7939 (tt0)
REVERT: B   93 TRP cc_start: 0.4666 (p-90) cc_final: 0.4302 (p-90)
REVERT: B  123 TYR cc_start: 0.7857 (m-80) cc_final: 0.6981 (m-80)
REVERT: B  132 TYR cc_start: 0.8263 (m-80) cc_final: 0.7840 (m-80)
REVERT: B  221 MET cc_start: 0.7891 (ptm) cc_final: 0.7604 (ppp)
REVERT: B  347 HIS cc_start: 0.8079 (m90) cc_final: 0.7733 (m-70)
REVERT: C  195 GLN cc_start: 0.7488 (pp30) cc_final: 0.6981 (pp30)
REVERT: D   74 ASP cc_start: 0.9265 (m-30) cc_final: 0.8991 (m-30)
REVERT: D  109 MET cc_start: 0.8987 (mtp) cc_final: 0.8763 (mtp)
REVERT: D  232 GLU cc_start: 0.9024 (mp0) cc_final: 0.8803 (mp0)
REVERT: E   50 MET cc_start: 0.8015 (ptm) cc_final: 0.7604 (ptm)
REVERT: P 1271 ASN cc_start: 0.7989 (t0) cc_final: 0.7365 (t0)
  outliers start: 2
  outliers final: 2
  residues processed: 197
  average time/residue: 0.3424
  time to fit residues: 103.5839
Evaluate side-chains
  162 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 160
  time to evaluate  : 1.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 28 optimal weight:    6.9990
   chunk 94 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   chunk 140 optimal weight:   10.0000
   chunk 49 optimal weight:    0.0970
   chunk 81 optimal weight:    0.6980
   chunk 147 optimal weight:   50.0000
   chunk 34 optimal weight:    0.5980
   chunk 170 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   overall best weight:    2.6782

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  36 ASN
** E  54 GLN ** 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 = 0.3671 r_free = 0.3671 target = 0.101609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.069131 restraints weight = 44793.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.069042 restraints weight = 28225.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.069674 restraints weight = 20053.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2960
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2960 r_free = 0.2960    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2960
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.2241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12793  Z= 0.160
  Angle     :  0.633  11.816  17440  Z= 0.338
  Chirality :  0.045   0.190   1951
  Planarity :  0.004   0.045   2338
  Dihedral  :  4.955  22.080   1878
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.23 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.35 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.99 (0.19), residues: 1729
  helix:  0.52 (0.27), residues: 328
  sheet: -1.09 (0.21), residues: 570
  loop : -2.26 (0.20), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 376 
 HIS   0.002   0.001   HIS A 186 
 PHE   0.022   0.002   PHE A 586 
 TYR   0.022   0.002   TYR D  67 
 ARG   0.012   0.001   ARG E  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03899 (  619)
  hydrogen bonds       : angle       5.49498 ( 1726)
  covalent geometry    : bond        0.00353 (12793)
  covalent geometry    : angle       0.63289 (17440)

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

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

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3458 Ramachandran restraints generated.
    1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 198
  time to evaluate  : 1.618 
Fit side-chains
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
REVERT: A  321 ARG cc_start: 0.7894 (mtm110) cc_final: 0.7655 (mtm-85)
REVERT: A  369 MET cc_start: 0.9046 (mmt) cc_final: 0.8709 (mmt)
REVERT: A  650 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8844 (mt-10)
REVERT: A  717 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7870 (tt0)
REVERT: A  780 LEU cc_start: 0.9341 (mm) cc_final: 0.9046 (mt)
REVERT: B  123 TYR cc_start: 0.7816 (m-80) cc_final: 0.6938 (m-80)
REVERT: B  221 MET cc_start: 0.7948 (ptm) cc_final: 0.7661 (ppp)
REVERT: B  347 HIS cc_start: 0.8065 (m90) cc_final: 0.7746 (m-70)
REVERT: C  195 GLN cc_start: 0.7472 (pp30) cc_final: 0.6964 (pp30)
REVERT: D   74 ASP cc_start: 0.9219 (m-30) cc_final: 0.8930 (m-30)
REVERT: D  105 ILE cc_start: 0.9262 (mm) cc_final: 0.8826 (mm)
REVERT: D  109 MET cc_start: 0.8927 (mtp) cc_final: 0.8663 (mtp)
REVERT: D  111 MET cc_start: 0.9531 (tpp) cc_final: 0.9307 (tpp)
REVERT: D  232 GLU cc_start: 0.8974 (mp0) cc_final: 0.8748 (mp0)
REVERT: E   50 MET cc_start: 0.7949 (ptm) cc_final: 0.7560 (ptm)
REVERT: P 1271 ASN cc_start: 0.7972 (t0) cc_final: 0.7409 (t0)
  outliers start: 2
  outliers final: 2
  residues processed: 200
  average time/residue: 0.2799
  time to fit residues: 85.7854
Evaluate side-chains
  161 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 159
  time to evaluate  : 2.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 144 optimal weight:   30.0000
   chunk 25 optimal weight:    3.9990
   chunk 15 optimal weight:    8.9990
   chunk 85 optimal weight:   10.0000
   chunk 145 optimal weight:   20.0000
   chunk 45 optimal weight:    1.9990
   chunk 138 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   chunk 24 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 116 optimal weight:   10.0000
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  36 ASN
** E  54 GLN ** 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 = 0.3655 r_free = 0.3655 target = 0.100753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.068171 restraints weight = 45096.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.068043 restraints weight = 29075.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.068630 restraints weight = 20805.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2940
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2940
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12793  Z= 0.201
  Angle     :  0.659  11.849  17440  Z= 0.352
  Chirality :  0.045   0.203   1951
  Planarity :  0.005   0.044   2338
  Dihedral  :  5.027  23.213   1878
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.21 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.09 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.03 (0.19), residues: 1729
  helix:  0.44 (0.27), residues: 328
  sheet: -1.06 (0.21), residues: 585
  loop : -2.34 (0.21), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B  93 
 HIS   0.002   0.001   HIS B 121 
 PHE   0.024   0.002   PHE A 586 
 TYR   0.024   0.002   TYR B 132 
 ARG   0.012   0.001   ARG E  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04024 (  619)
  hydrogen bonds       : angle       5.56015 ( 1726)
  covalent geometry    : bond        0.00443 (12793)
  covalent geometry    : angle       0.65948 (17440)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5092.34 seconds
wall clock time: 91 minutes 22.25 seconds (5482.25 seconds total)