Starting phenix.real_space_refine
on Sat May 17 16:39:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k9r_62196/05_2025/9k9r_62196.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k9r_62196/05_2025/9k9r_62196.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k9r_62196/05_2025/9k9r_62196.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k9r_62196/05_2025/9k9r_62196.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k9r_62196/05_2025/9k9r_62196.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k9r_62196/05_2025/9k9r_62196.cif"
  }
  resolution = 2.61
  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=   0.001 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2132 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      43      5.49       5
     Mg      1      5.21       5
     S      71      5.16       5
     C    8989      2.51       5
     N    2363      2.21       5
     O    2763      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 14230
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 8207
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1005, 8207
          Classifications: {'peptide': 1005}
          Link IDs: {'PTRANS': 37, 'TRANS': 967}
    Chain: "B"
      Number of atoms: 1767
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1767
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "C"
      Number of atoms: 3415
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 419, 3415
          Classifications: {'peptide': 419}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 408}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "P"
      Number of atoms: 287
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 287
          Classifications: {'DNA': 14}
          Link IDs: {'rna3p': 13}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "T"
      Number of atoms: 41
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 41
          Classifications: {'DNA': 2}
          Link IDs: {'rna3p': 1}
    Chain: "T"
      Number of atoms: 483
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 23, 463
          Unusual residues: {'ORP': 1}
          Classifications: {'DNA': 22, 'undetermined': 1}
          Link IDs: {'rna3p': 21, None: 1}
            Not linked:
              pdbres="ORP T   5 "
              pdbres=" DC T   6 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
      Conformer: "B"
        Number of residues, atoms: 23, 463
          Unusual residues: {'ORP': 1}
          Classifications: {'DNA': 22, 'undetermined': 1}
          Link IDs: {'rna3p': 21, None: 1}
            Not linked:
              pdbres="ORP T   5 "
              pdbres=" DC T   6 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          bond proxies already assigned to first conformer: 495
    Chain: "A"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 30
          Unusual residues: {' MG': 1, 'TTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" P  A DT T  11 " occ=0.50
      ... (38 atoms not shown)
      pdb=" C6 B DT T  11 " occ=0.50
  Time building chain proxies: 8.71, per 1000 atoms: 0.61
  Number of scatterers: 14230
  At special positions: 0
  Unit cell: (99.45, 124.95, 145.35, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      71     16.00
     P      43     15.00
     Mg      1     11.99
     O    2763      8.00
     N    2363      7.00
     C    8989      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.74
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  3268 Ramachandran restraints generated.
    1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3146

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 21 sheets defined
      39.0% alpha, 20.6% beta
      13 base pairs and 26 stacking pairs defined.
    Time for finding SS restraints: 4.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 48
    Processing helix  chain 'A' and resid 108 through 118
    Processing helix  chain 'A' and resid 128 through 130
      No H-bonds generated for 'chain 'A' and resid 128 through 130'
    Processing helix  chain 'A' and resid 144 through 149
    Processing helix  chain 'A' and resid 209 through 220
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 3.504A  pdb=" N   GLU A 229 " --> pdb=" O   SER A 226 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   MET A 230 " --> pdb=" O   LEU A 227 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 226 through 230'
    Processing helix  chain 'A' and resid 240 through 253
    Processing helix  chain 'A' and resid 267 through 280
    Processing helix  chain 'A' and resid 331 through 339
    Processing helix  chain 'A' and resid 345 through 354
    Processing helix  chain 'A' and resid 380 through 389
    Processing helix  chain 'A' and resid 439 through 446
    Processing helix  chain 'A' and resid 448 through 473
      removed outlier: 3.859A  pdb=" N   CYS A 466 " --> pdb=" O   ASP A 462 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   GLN A 467 " --> pdb=" O   ALA A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 487
    Processing helix  chain 'A' and resid 497 through 502
      removed outlier: 3.567A  pdb=" N   ILE A 502 " --> pdb=" O   ALA A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 514
      removed outlier: 3.515A  pdb=" N   LEU A 506 " --> pdb=" O   ILE A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 562
    Processing helix  chain 'A' and resid 564 through 566
      No H-bonds generated for 'chain 'A' and resid 564 through 566'
    Processing helix  chain 'A' and resid 576 through 591
      removed outlier: 4.029A  pdb=" N   GLN A 589 " --> pdb=" O   GLN A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 643
      removed outlier: 3.959A  pdb=" N   ARG A 625 " --> pdb=" O   GLY A 621 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   GLN A 643 " --> pdb=" O   LYS A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 646 through 672
      removed outlier: 3.801A  pdb=" N   TYR A 668 " --> pdb=" O   ALA A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 703
    Processing helix  chain 'A' and resid 763 through 782
      removed outlier: 3.795A  pdb=" N   SER A 767 " --> pdb=" O   ASP A 763 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 837 through 857
    Processing helix  chain 'A' and resid 862 through 883
    Processing helix  chain 'A' and resid 886 through 891
      removed outlier: 3.560A  pdb=" N   LEU A 889 " --> pdb=" O   PRO A 886 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   MET A 891 " --> pdb=" O   GLU A 888 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 905 through 918
    Processing helix  chain 'A' and resid 947 through 949
      No H-bonds generated for 'chain 'A' and resid 947 through 949'
    Processing helix  chain 'A' and resid 967 through 981
      removed outlier: 4.472A  pdb=" N   TYR A 971 " --> pdb=" O   PHE A 967 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 986 through 998
    Processing helix  chain 'B' and resid 16 through 20
    Processing helix  chain 'B' and resid 22 through 31
    Processing helix  chain 'B' and resid 33 through 38
    Processing helix  chain 'B' and resid 45 through 49
    Processing helix  chain 'B' and resid 86 through 101
    Processing helix  chain 'B' and resid 133 through 150
      removed outlier: 5.553A  pdb=" N   LYS B 139 " --> pdb=" O   ILE B 135 " (cutoff:3.500A)
      removed outlier: 5.525A  pdb=" N   ILE B 140 " --> pdb=" O   TYR B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 205
    Processing helix  chain 'C' and resid 3 through 19
    Processing helix  chain 'C' and resid 24 through 43
    Processing helix  chain 'C' and resid 57 through 61
    Processing helix  chain 'C' and resid 107 through 121
      removed outlier: 3.675A  pdb=" N   ASP C 121 " --> pdb=" O   VAL C 117 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 149 through 159
      removed outlier: 3.585A  pdb=" N   GLY C 159 " --> pdb=" O   ALA C 155 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 177 through 189
      removed outlier: 3.511A  pdb=" N   ASP C 189 " --> pdb=" O   GLU C 185 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 249 through 257
    Processing helix  chain 'C' and resid 286 through 298
      removed outlier: 3.925A  pdb=" N   ILE C 294 " --> pdb=" O   ILE C 290 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 315 through 321
    Processing helix  chain 'C' and resid 331 through 334
    Processing helix  chain 'C' and resid 335 through 341
      removed outlier: 3.909A  pdb=" N   ASN C 339 " --> pdb=" O   VAL C 335 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LYS C 340 " --> pdb=" O   ASP C 336 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   SER C 341 " --> pdb=" O   GLU C 337 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 335 through 341'
    Processing helix  chain 'C' and resid 341 through 351
    Processing helix  chain 'C' and resid 353 through 361
    Processing helix  chain 'C' and resid 365 through 373
    Processing helix  chain 'C' and resid 393 through 396
    Processing helix  chain 'C' and resid 397 through 406
      removed outlier: 4.145A  pdb=" N   ASN C 406 " --> pdb=" O   THR C 402 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 406 through 424
      removed outlier: 3.608A  pdb=" N   ARG C 423 " --> pdb=" O   ASP C 419 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126
      removed outlier: 5.579A  pdb=" N   CYS A   5 " --> pdb=" O   ARG A  23 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   ARG A  23 " --> pdb=" O   CYS A   5 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ASN A   7 " --> pdb=" O   LYS A  21 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   PHE A  17 " --> pdb=" O   SER A  11 " (cutoff:3.500A)
      removed outlier: 8.379A  pdb=" N   TYR A 140 " --> pdb=" O   THR A  29 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   PHE A  31 " --> pdb=" O   TYR A 140 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   CYS A 142 " --> pdb=" O   PHE A  31 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   ARG A  33 " --> pdb=" O   CYS A 142 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   HIS A 141 " --> pdb=" O   LYS A 134 " (cutoff:3.500A)
      removed outlier: 5.755A  pdb=" N   LYS A 134 " --> pdb=" O   HIS A 141 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43
      removed outlier: 6.300A  pdb=" N   SER A  84 " --> pdb=" O   ARG A  64 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   ARG A  64 " --> pdb=" O   SER A  84 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   ALA A  86 " --> pdb=" O   LYS A  62 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   LYS A  62 " --> pdb=" O   ALA A  86 " (cutoff:3.500A)
      removed outlier: 5.703A  pdb=" N   MET A  88 " --> pdb=" O   MET A  60 " (cutoff:3.500A)
      removed outlier: 8.489A  pdb=" N   ILE A 516 " --> pdb=" O   LYS A  62 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   ARG A  64 " --> pdb=" O   ILE A 516 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   VAL A 518 " --> pdb=" O   ARG A  64 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   ILE A  66 " --> pdb=" O   VAL A 518 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73
      removed outlier: 6.629A  pdb=" N   SER A  73 " --> pdb=" O   VAL A 573 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   LEU A 568 " --> pdb=" O   ASP A 616 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   ASP A 616 " --> pdb=" O   LEU A 568 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLY A 570 " --> pdb=" O   ILE A 614 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   SER A 574 " --> pdb=" O   SER A 610 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   SER A 610 " --> pdb=" O   SER A 574 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223
      removed outlier: 6.289A  pdb=" N   LEU A 222 " --> pdb=" O   LEU A 238 " (cutoff:3.500A)
      removed outlier: 8.111A  pdb=" N   VAL A 237 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   THR A 201 " --> pdb=" O   VAL A 237 " (cutoff:3.500A)
      removed outlier: 7.474A  pdb=" N   CYS A 239 " --> pdb=" O   THR A 201 " (cutoff:3.500A)
      removed outlier: 5.616A  pdb=" N   ILE A 203 " --> pdb=" O   CYS A 239 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   SER A 184 " --> pdb=" O   ASN A 204 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   LEU A 163 " --> pdb=" O   VAL A 260 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 285 through 287
    Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 305
    Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 362
      removed outlier: 6.607A  pdb=" N   THR A 369 " --> pdb=" O   LEU A 361 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   LYS A 416 " --> pdb=" O   LYS A 408 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   LYS A 408 " --> pdb=" O   LYS A 416 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   VAL A 418 " --> pdb=" O   ILE A 406 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   LYS A 404 " --> pdb=" O   SER A 420 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 732 through 734
      removed outlier: 6.876A  pdb=" N   PHE A 756 " --> pdb=" O   VAL A 748 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   ALA A 793 " --> pdb=" O   ILE A 547 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   ASP A 549 " --> pdb=" O   PHE A 791 " (cutoff:3.500A)
      removed outlier: 5.526A  pdb=" N   PHE A 791 " --> pdb=" O   ASP A 549 " (cutoff:3.500A)
      removed outlier: 5.547A  pdb=" N   TYR A 795 " --> pdb=" O   TYR A 811 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   TYR A 811 " --> pdb=" O   TYR A 795 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   ASN A 797 " --> pdb=" O   MET A 809 " (cutoff:3.500A)
      removed outlier: 4.971A  pdb=" N   MET A 809 " --> pdb=" O   ASN A 797 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   LYS A 805 " --> pdb=" O   GLN A 801 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 892 through 895
    Processing sheet with id=AB1, first strand: chain 'A' and resid 892 through 895
    Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 5
    Processing sheet with id=AB3, first strand: chain 'B' and resid 42 through 43
    Processing sheet with id=AB4, first strand: chain 'B' and resid 116 through 120
      removed outlier: 6.568A  pdb=" N   VAL B  62 " --> pdb=" O   ILE B 117 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   TRP B 119 " --> pdb=" O   VAL B  62 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   VAL B  64 " --> pdb=" O   TRP B 119 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   CYS B  63 " --> pdb=" O   TYR B 156 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   LEU B 158 " --> pdb=" O   CYS B  63 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   CYS B  65 " --> pdb=" O   LEU B 158 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 107 through 108
      removed outlier: 3.843A  pdb=" N   GLY B 107 " --> pdb=" O   ILE B 217 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 69 through 71
    Processing sheet with id=AB7, first strand: chain 'C' and resid 166 through 168
      removed outlier: 4.204A  pdb=" N   SER C 196 " --> pdb=" O   VAL C  81 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLN C 208 " --> pdb=" O   TYR C 199 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 96 through 97
      removed outlier: 3.555A  pdb=" N   VAL C  96 " --> pdb=" O   ILE C  88 " (cutoff:3.500A)
      removed outlier: 5.596A  pdb=" N   VAL C 130 " --> pdb=" O   MET C 138 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   MET C 138 " --> pdb=" O   VAL C 130 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 214 through 219
    Processing sheet with id=AC1, first strand: chain 'C' and resid 222 through 229
      removed outlier: 4.077A  pdb=" N   SER C 222 " --> pdb=" O   ILE C 238 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ILE C 238 " --> pdb=" O   SER C 222 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ILE C 228 " --> pdb=" O   ILE C 232 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   ILE C 232 " --> pdb=" O   ILE C 228 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 302 through 304
    Processing sheet with id=AC3, first strand: chain 'C' and resid 375 through 380
      removed outlier: 6.344A  pdb=" N   GLU C 380 " --> pdb=" O   VAL C 384 " (cutoff:3.500A)
      removed outlier: 5.276A  pdb=" N   VAL C 384 " --> pdb=" O   GLU C 380 " (cutoff:3.500A)

    585 hydrogen bonds defined for protein.
    1653 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      31 hydrogen bonds
      62 hydrogen bond angles
      0 basepair planarities
      13 basepair parallelities
      27 stacking parallelities
  Total time for adding SS restraints: 5.27

  Time building geometry restraints manager: 4.23 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: 3699
        1.33 -     1.45: 2841
        1.45 -     1.57: 7886
        1.57 -     1.69: 84
        1.69 -     1.81: 108
  Bond restraints: 14618
  Sorted by residual:
  bond pdb=" N   VAL C  50 "
       pdb=" CA  VAL C  50 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.034 1.20e-02 6.94e+03 8.26e+00
  bond pdb=" N   LYS C  49 "
       pdb=" CA  LYS C  49 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.033 1.22e-02 6.72e+03 7.21e+00
  bond pdb=" C5  TTP A1102 "
       pdb=" C6  TTP A1102 "
    ideal  model  delta    sigma   weight residual
    1.390  1.339  0.051 2.00e-02 2.50e+03 6.63e+00
  bond pdb=" N   ASP B  68 "
       pdb=" CA  ASP B  68 "
    ideal  model  delta    sigma   weight residual
    1.456  1.481 -0.025 1.04e-02 9.25e+03 5.96e+00
  bond pdb=" N   ARG B 185 "
       pdb=" CA  ARG B 185 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.032 1.34e-02 5.57e+03 5.83e+00
  ... (remaining 14613 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.21: 19841
        3.21 -     6.42: 78
        6.42 -     9.63: 7
        9.63 -    12.84: 1
       12.84 -    16.05: 2
  Bond angle restraints: 19929
  Sorted by residual:
  angle pdb=" PA  TTP A1102 "
        pdb=" O3A TTP A1102 "
        pdb=" PB  TTP A1102 "
      ideal   model   delta    sigma   weight residual
     120.50  136.55  -16.05 3.00e+00 1.11e-01 2.86e+01
  angle pdb=" PB  TTP A1102 "
        pdb=" O3B TTP A1102 "
        pdb=" PG  TTP A1102 "
      ideal   model   delta    sigma   weight residual
     120.50  133.71  -13.21 3.00e+00 1.11e-01 1.94e+01
  angle pdb=" N   ILE C 228 "
        pdb=" CA  ILE C 228 "
        pdb=" C   ILE C 228 "
      ideal   model   delta    sigma   weight residual
     113.71  109.66    4.05 9.50e-01 1.11e+00 1.82e+01
  angle pdb=" CA  ARG B 185 "
        pdb=" C   ARG B 185 "
        pdb=" O   ARG B 185 "
      ideal   model   delta    sigma   weight residual
     122.01  117.71    4.30 1.05e+00 9.07e-01 1.67e+01
  angle pdb=" N   ASP B 186 "
        pdb=" CA  ASP B 186 "
        pdb=" C   ASP B 186 "
      ideal   model   delta    sigma   weight residual
     113.23  108.37    4.86 1.22e+00 6.72e-01 1.59e+01
  ... (remaining 19924 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.76: 8277
       28.76 -    57.53: 428
       57.53 -    86.29: 35
       86.29 -   115.06: 2
      115.06 -   143.82: 2
  Dihedral angle restraints: 8744
    sinusoidal: 3867
      harmonic: 4877
  Sorted by residual:
  dihedral pdb=" C2  TTP A1102 "
           pdb=" C1' TTP A1102 "
           pdb=" N1  TTP A1102 "
           pdb=" O4' TTP A1102 "
      ideal   model   delta sinusoidal    sigma   weight residual
     301.68  157.86  143.82     1      2.00e+01 2.50e-03 4.34e+01
  dihedral pdb=" O3B TTP A1102 "
           pdb=" O3A TTP A1102 "
           pdb=" PB  TTP A1102 "
           pdb=" PA  TTP A1102 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00   55.62  124.38     1      2.00e+01 2.50e-03 3.76e+01
  dihedral pdb=" C5' TTP A1102 "
           pdb=" O5' TTP A1102 "
           pdb=" PA  TTP A1102 "
           pdb=" O3A TTP A1102 "
      ideal   model   delta sinusoidal    sigma   weight residual
     179.97   83.31   96.67     1      2.00e+01 2.50e-03 2.68e+01
  ... (remaining 8741 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1710
       0.049 -    0.098: 398
       0.098 -    0.147: 95
       0.147 -    0.195: 3
       0.195 -    0.244: 2
  Chirality restraints: 2208
  Sorted by residual:
  chirality pdb=" CB  VAL A 310 "
            pdb=" CA  VAL A 310 "
            pdb=" CG1 VAL A 310 "
            pdb=" CG2 VAL A 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.24 2.00e-01 2.50e+01 1.49e+00
  chirality pdb=" CB  VAL A 365 "
            pdb=" CA  VAL A 365 "
            pdb=" CG1 VAL A 365 "
            pdb=" CG2 VAL A 365 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" C3' TTP A1102 "
            pdb=" C2' TTP A1102 "
            pdb=" C4' TTP A1102 "
            pdb=" O3' TTP A1102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.67    0.16 2.00e-01 2.50e+01 6.19e-01
  ... (remaining 2205 not shown)

  Planarity restraints: 2391
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B  45 "   -0.033 5.00e-02 4.00e+02   5.07e-02 4.11e+00
        pdb=" N   PRO B  46 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO B  46 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B  46 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 592 "    0.029 5.00e-02 4.00e+02   4.39e-02 3.08e+00
        pdb=" N   PRO A 593 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 593 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 593 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B  70 "   -0.026 5.00e-02 4.00e+02   3.99e-02 2.54e+00
        pdb=" N   PRO B  71 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B  71 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B  71 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 2388 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 252
        2.67 -     3.23: 12928
        3.23 -     3.79: 20947
        3.79 -     4.34: 29004
        4.34 -     4.90: 47886
  Nonbonded interactions: 111017
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 373 "
            pdb=" N   ASP A 374 "
     model   vdw
     2.117 3.120
  nonbonded pdb=" OD1 ASP C 249 "
            pdb=" N   VAL C 250 "
     model   vdw
     2.161 3.120
  nonbonded pdb=" O   ILE C 313 "
            pdb=" NE2 GLN C 409 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" OH  TYR A 749 "
            pdb=" O   LYS A 803 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   VAL C 411 "
            pdb=" ND2 ASN C 415 "
     model   vdw
     2.236 3.120
  ... (remaining 111012 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 individual isotropic
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:             1.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.110
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.630
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     36.390
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.950
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
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      :  0.005   0.053  14620  Z= 0.215
  Angle     :  0.630  16.049  19929  Z= 0.335
  Chirality :  0.044   0.244   2208
  Planarity :  0.004   0.051   2391
  Dihedral  : 15.937 143.820   5598
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  4.28 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.40 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.21), residues: 1634
  helix:  1.38 (0.22), residues: 580
  sheet:  0.66 (0.29), residues: 346
  loop : -1.33 (0.22), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 470 
 HIS   0.006   0.001   HIS A 170 
 PHE   0.020   0.002   PHE A 838 
 TYR   0.019   0.001   TYR A 528 
 ARG   0.003   0.000   ARG A  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14255 (  612)
  hydrogen bonds       : angle       5.52221 ( 1715)
  covalent geometry    : bond        0.00478 (14618)
  covalent geometry    : angle       0.63009 (19929)
  Misc. bond           : bond        0.03910 (    2)

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

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

  3268 Ramachandran restraints generated.
    1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3268 Ramachandran restraints generated.
    1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  339 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 338
  time to evaluate  : 1.398 
Fit side-chains
   revert: symmetry clash
REVERT: A  209 THR cc_start: 0.8166 (m) cc_final: 0.7884 (m)
REVERT: A  291 LYS cc_start: 0.7898 (mmtm) cc_final: 0.7655 (mmtm)
REVERT: A  310 VAL cc_start: 0.8381 (p) cc_final: 0.8102 (t)
REVERT: A  792 GLU cc_start: 0.7288 (mm-30) cc_final: 0.7047 (mm-30)
REVERT: A  943 LYS cc_start: 0.8065 (mmtp) cc_final: 0.7811 (mmtp)
REVERT: B  109 ASN cc_start: 0.7957 (t0) cc_final: 0.7757 (t0)
REVERT: B  205 ASP cc_start: 0.7552 (t0) cc_final: 0.7136 (t0)
REVERT: C   11 LYS cc_start: 0.8429 (mttm) cc_final: 0.8223 (mttp)
REVERT: C   95 MET cc_start: 0.2994 (mmp) cc_final: 0.2169 (mmp)
REVERT: C  184 MET cc_start: 0.8039 (mmp) cc_final: 0.7720 (mmp)
REVERT: C  224 LYS cc_start: 0.7787 (ptpp) cc_final: 0.7502 (ptpp)
REVERT: C  350 ASN cc_start: 0.7501 (m110) cc_final: 0.7194 (m110)
REVERT: C  422 LYS cc_start: 0.8153 (tptp) cc_final: 0.7834 (tptp)
  outliers start: 1
  outliers final: 0
  residues processed: 338
  average time/residue: 1.2679
  time to fit residues: 469.3805
Evaluate side-chains
  314 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 314
  time to evaluate  : 1.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 139 optimal weight:   10.0000
   chunk 125 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 84 optimal weight:    0.5980
   chunk 66 optimal weight:    0.5980
   chunk 129 optimal weight:   20.0000
   chunk 50 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9980
   chunk 96 optimal weight:    2.9990
   chunk 149 optimal weight:   30.0000
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
A 214 GLN
A 413 ASN
A 442 GLN
B 111 ASN
B 206 ASN
C   9 ASN
C 304 ASN
C 373 ASN
C 391 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.167347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.128266 restraints weight = 22667.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 2.21
r_work: 0.3433 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3281 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3280
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3280 r_free = 0.3280    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3280 r_free = 0.3280    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3280
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.1001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  14620  Z= 0.156
  Angle     :  0.570   9.626  19929  Z= 0.304
  Chirality :  0.042   0.188   2208
  Planarity :  0.004   0.053   2391
  Dihedral  : 14.978 137.288   2277
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.79 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  9.37 %
    Favored  : 89.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.21), residues: 1634
  helix:  1.61 (0.22), residues: 588
  sheet:  0.69 (0.28), residues: 347
  loop : -1.33 (0.22), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 470 
 HIS   0.005   0.001   HIS A 839 
 PHE   0.016   0.001   PHE A 838 
 TYR   0.018   0.001   TYR A 190 
 ARG   0.004   0.000   ARG A 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04889 (  612)
  hydrogen bonds       : angle       4.44294 ( 1715)
  covalent geometry    : bond        0.00364 (14618)
  covalent geometry    : angle       0.57016 (19929)
  Misc. bond           : bond        0.00055 (    2)

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

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

  3268 Ramachandran restraints generated.
    1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3268 Ramachandran restraints generated.
    1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  347 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 328
  time to evaluate  : 1.487 
Fit side-chains
REVERT: A   88 MET cc_start: 0.8769 (mmt) cc_final: 0.8499 (mmt)
REVERT: A  209 THR cc_start: 0.8464 (m) cc_final: 0.8241 (m)
REVERT: A  291 LYS cc_start: 0.8238 (mmtm) cc_final: 0.8009 (mmtm)
REVERT: A  413 ASN cc_start: 0.7789 (t0) cc_final: 0.7462 (t160)
REVERT: A  742 ARG cc_start: 0.7900 (ttm-80) cc_final: 0.7588 (ttm-80)
REVERT: A  832 ARG cc_start: 0.8329 (mtp180) cc_final: 0.8124 (mtt180)
REVERT: B   96 ILE cc_start: 0.8026 (tp) cc_final: 0.7750 (tp)
REVERT: B  205 ASP cc_start: 0.8096 (t0) cc_final: 0.7647 (t0)
REVERT: C   32 ASN cc_start: 0.7975 (m110) cc_final: 0.7695 (m-40)
REVERT: C   95 MET cc_start: 0.3773 (mmp) cc_final: 0.2695 (mmp)
REVERT: C  184 MET cc_start: 0.8499 (mmp) cc_final: 0.8105 (mmp)
REVERT: C  224 LYS cc_start: 0.7667 (ptpp) cc_final: 0.7372 (ptpp)
REVERT: C  336 ASP cc_start: 0.7970 (m-30) cc_final: 0.7698 (m-30)
REVERT: C  373 ASN cc_start: 0.7157 (m-40) cc_final: 0.6898 (m110)
REVERT: C  422 LYS cc_start: 0.8134 (tptp) cc_final: 0.7745 (tptp)
  outliers start: 19
  outliers final: 7
  residues processed: 330
  average time/residue: 1.2637
  time to fit residues: 456.3124
Evaluate side-chains
  320 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 313
  time to evaluate  : 1.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain A residue  640 MET
Chi-restraints excluded: chain A residue  688 THR
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain B residue   77 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0060
   chunk 70 optimal weight:    1.9990
   chunk 90 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 132 optimal weight:   30.0000
   chunk 2 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN
A 204 ASN
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 214 GLN
A 801 GLN
A 816 ASN
A 981 ASN
B 109 ASN
B 111 ASN
C  32 ASN
C 350 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.167706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.126453 restraints weight = 29545.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 2.60
r_work: 0.3400 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3400
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3400 r_free = 0.3400    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3400 r_free = 0.3400    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3400
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.1256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14620  Z= 0.137
  Angle     :  0.532   8.752  19929  Z= 0.285
  Chirality :  0.041   0.262   2208
  Planarity :  0.004   0.051   2391
  Dihedral  : 14.903 138.158   2277
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.10 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 11.42 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.21), residues: 1634
  helix:  1.73 (0.22), residues: 588
  sheet:  0.61 (0.28), residues: 362
  loop : -1.32 (0.22), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 470 
 HIS   0.005   0.001   HIS A 839 
 PHE   0.013   0.001   PHE A 838 
 TYR   0.017   0.001   TYR A 190 
 ARG   0.002   0.000   ARG A 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04485 (  612)
  hydrogen bonds       : angle       4.26737 ( 1715)
  covalent geometry    : bond        0.00315 (14618)
  covalent geometry    : angle       0.53203 (19929)
  Misc. bond           : bond        0.00034 (    2)

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

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

  3268 Ramachandran restraints generated.
    1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3268 Ramachandran restraints generated.
    1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  361 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 332
  time to evaluate  : 1.508 
Fit side-chains
REVERT: A   88 MET cc_start: 0.8696 (mmt) cc_final: 0.8416 (mmt)
REVERT: A  209 THR cc_start: 0.8325 (m) cc_final: 0.8123 (m)
REVERT: A  225 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8441 (mt0)
REVERT: A  291 LYS cc_start: 0.8119 (mmtm) cc_final: 0.7879 (mmtm)
REVERT: A  413 ASN cc_start: 0.7669 (t0) cc_final: 0.7368 (t0)
REVERT: A  540 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7972 (mtt)
REVERT: A  742 ARG cc_start: 0.7632 (ttm-80) cc_final: 0.7325 (ttm-80)
REVERT: B   96 ILE cc_start: 0.7956 (tp) cc_final: 0.7643 (tp)
REVERT: B  205 ASP cc_start: 0.7857 (t0) cc_final: 0.7431 (t0)
REVERT: C   32 ASN cc_start: 0.7841 (m-40) cc_final: 0.7554 (m-40)
REVERT: C   95 MET cc_start: 0.3741 (mmp) cc_final: 0.2726 (mmp)
REVERT: C  184 MET cc_start: 0.8427 (mmp) cc_final: 0.8019 (mmp)
REVERT: C  224 LYS cc_start: 0.7700 (ptpp) cc_final: 0.7399 (ptpp)
REVERT: C  336 ASP cc_start: 0.7942 (m-30) cc_final: 0.7631 (m-30)
REVERT: C  373 ASN cc_start: 0.7067 (m-40) cc_final: 0.6865 (m110)
REVERT: C  397 ASN cc_start: 0.7972 (t0) cc_final: 0.7716 (t0)
REVERT: C  419 ASP cc_start: 0.7413 (p0) cc_final: 0.7108 (p0)
REVERT: C  422 LYS cc_start: 0.8027 (tptp) cc_final: 0.7619 (tptp)
  outliers start: 29
  outliers final: 14
  residues processed: 336
  average time/residue: 1.2412
  time to fit residues: 456.7083
Evaluate side-chains
  333 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 317
  time to evaluate  : 1.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 GLN
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  337 LYS
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  445 LYS
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain A residue  540 MET
Chi-restraints excluded: chain A residue  646 SER
Chi-restraints excluded: chain A residue  688 THR
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  959 LYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue  345 LYS
Chi-restraints excluded: chain C residue  365 GLU
Chi-restraints excluded: chain C residue  379 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 151 optimal weight:    9.9990
   chunk 125 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 140 optimal weight:    0.5980
   chunk 98 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 121 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 214 GLN
A 556 ASN
A 801 GLN
A 899 ASN
A 981 ASN
B 111 ASN
B 120 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.166674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.127400 restraints weight = 20278.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 2.03
r_work: 0.3424 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3273
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3273 r_free = 0.3273    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3273 r_free = 0.3273    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3273
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.1349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  14620  Z= 0.181
  Angle     :  0.566  11.404  19929  Z= 0.301
  Chirality :  0.043   0.300   2208
  Planarity :  0.004   0.052   2391
  Dihedral  : 14.961 137.096   2277
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.22 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 13.27 %
    Favored  : 84.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.21), residues: 1634
  helix:  1.68 (0.22), residues: 588
  sheet:  0.54 (0.27), residues: 374
  loop : -1.34 (0.22), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 470 
 HIS   0.006   0.001   HIS A 839 
 PHE   0.015   0.001   PHE A 838 
 TYR   0.019   0.001   TYR A 190 
 ARG   0.002   0.000   ARG A  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05093 (  612)
  hydrogen bonds       : angle       4.31752 ( 1715)
  covalent geometry    : bond        0.00431 (14618)
  covalent geometry    : angle       0.56606 (19929)
  Misc. bond           : bond        0.00060 (    2)

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

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

  3268 Ramachandran restraints generated.
    1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3268 Ramachandran restraints generated.
    1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  361 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 328
  time to evaluate  : 1.502 
Fit side-chains
REVERT: A   88 MET cc_start: 0.8772 (mmt) cc_final: 0.8553 (mmt)
REVERT: A  225 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8570 (mt0)
REVERT: A  291 LYS cc_start: 0.8236 (mmtm) cc_final: 0.8000 (mmtm)
REVERT: A  413 ASN cc_start: 0.7790 (t0) cc_final: 0.7394 (t0)
REVERT: A  540 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8214 (mtt)
REVERT: A  742 ARG cc_start: 0.7934 (ttm-80) cc_final: 0.7666 (ttm-80)
REVERT: A  837 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7938 (ttpp)
REVERT: B   96 ILE cc_start: 0.8068 (tp) cc_final: 0.7755 (tp)
REVERT: B  205 ASP cc_start: 0.8081 (t0) cc_final: 0.7673 (t0)
REVERT: C    9 ASN cc_start: 0.7959 (m-40) cc_final: 0.7560 (m110)
REVERT: C   21 ARG cc_start: 0.7095 (ptm160) cc_final: 0.6354 (ptm160)
REVERT: C   32 ASN cc_start: 0.8139 (m-40) cc_final: 0.7859 (m-40)
REVERT: C   95 MET cc_start: 0.3713 (mmp) cc_final: 0.2715 (mmp)
REVERT: C  184 MET cc_start: 0.8462 (mmp) cc_final: 0.8058 (mmp)
REVERT: C  224 LYS cc_start: 0.7739 (ptpp) cc_final: 0.7438 (ptpp)
REVERT: C  336 ASP cc_start: 0.8052 (m-30) cc_final: 0.7716 (m-30)
REVERT: C  349 LYS cc_start: 0.8624 (mmmm) cc_final: 0.8390 (mmmm)
REVERT: C  422 LYS cc_start: 0.8057 (tptp) cc_final: 0.7675 (tptp)
  outliers start: 33
  outliers final: 17
  residues processed: 334
  average time/residue: 1.2251
  time to fit residues: 448.4844
Evaluate side-chains
  339 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 319
  time to evaluate  : 1.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  215 GLU
Chi-restraints excluded: chain A residue  225 GLN
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  337 LYS
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  445 LYS
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain A residue  540 MET
Chi-restraints excluded: chain A residue  646 SER
Chi-restraints excluded: chain A residue  688 THR
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  837 LYS
Chi-restraints excluded: chain A residue  945 VAL
Chi-restraints excluded: chain B residue   48 LYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain C residue  345 LYS
Chi-restraints excluded: chain C residue  365 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 149 optimal weight:   10.0000
   chunk 159 optimal weight:    4.9990
   chunk 129 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 130 optimal weight:    6.9990
   chunk 121 optimal weight:    3.9990
   chunk 111 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 123 optimal weight:    0.8980
   chunk 120 optimal weight:    0.0970
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
A 211 GLN
A 214 GLN
A 709 ASN
A 801 GLN
A 816 ASN
B 109 ASN
C 373 ASN
C 397 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.164605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.125119 restraints weight = 20406.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 2.13
r_work: 0.3384 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.066  14620  Z= 0.287
  Angle     :  0.637  11.049  19929  Z= 0.338
  Chirality :  0.047   0.333   2208
  Planarity :  0.005   0.056   2391
  Dihedral  : 15.241 136.202   2277
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.35 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.65 %
    Favored  : 82.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.21), residues: 1634
  helix:  1.48 (0.22), residues: 594
  sheet:  0.49 (0.27), residues: 378
  loop : -1.42 (0.23), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 470 
 HIS   0.008   0.001   HIS A 170 
 PHE   0.018   0.002   PHE A 560 
 TYR   0.025   0.002   TYR A 528 
 ARG   0.005   0.000   ARG A  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06219 (  612)
  hydrogen bonds       : angle       4.47172 ( 1715)
  covalent geometry    : bond        0.00698 (14618)
  covalent geometry    : angle       0.63698 (19929)
  Misc. bond           : bond        0.00111 (    2)

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

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

  3268 Ramachandran restraints generated.
    1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3268 Ramachandran restraints generated.
    1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  368 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 332
  time to evaluate  : 1.812 
Fit side-chains
REVERT: A  225 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8577 (mt0)
REVERT: A  230 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7125 (tpp)
REVERT: A  291 LYS cc_start: 0.8270 (mmtm) cc_final: 0.8032 (mmtm)
REVERT: A  310 VAL cc_start: 0.8589 (p) cc_final: 0.8384 (t)
REVERT: A  341 LEU cc_start: 0.8986 (mt) cc_final: 0.8764 (mt)
REVERT: A  373 ASP cc_start: 0.8018 (t0) cc_final: 0.7719 (t0)
REVERT: A  413 ASN cc_start: 0.7819 (t0) cc_final: 0.7482 (t0)
REVERT: A  742 ARG cc_start: 0.7959 (ttm-80) cc_final: 0.7701 (ttm-80)
REVERT: A  800 MET cc_start: 0.8820 (mmt) cc_final: 0.8491 (mtt)
REVERT: A  837 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7983 (ttpp)
REVERT: A  842 MET cc_start: 0.8742 (mmp) cc_final: 0.8513 (mmm)
REVERT: A  943 LYS cc_start: 0.8559 (mmtp) cc_final: 0.8338 (mmtp)
REVERT: B   96 ILE cc_start: 0.8194 (tp) cc_final: 0.7872 (tp)
REVERT: B  205 ASP cc_start: 0.8146 (t0) cc_final: 0.7732 (t0)
REVERT: C   32 ASN cc_start: 0.8163 (m-40) cc_final: 0.7850 (m-40)
REVERT: C   95 MET cc_start: 0.3373 (mmp) cc_final: 0.2371 (mmp)
REVERT: C  184 MET cc_start: 0.8472 (mmp) cc_final: 0.8065 (mmp)
REVERT: C  224 LYS cc_start: 0.7755 (ptpp) cc_final: 0.7450 (ptpp)
REVERT: C  336 ASP cc_start: 0.8101 (m-30) cc_final: 0.7748 (m-30)
REVERT: C  422 LYS cc_start: 0.8146 (tptp) cc_final: 0.7826 (tptp)
  outliers start: 36
  outliers final: 24
  residues processed: 339
  average time/residue: 1.2607
  time to fit residues: 469.8043
Evaluate side-chains
  346 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 319
  time to evaluate  : 1.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  143 ASP
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  215 GLU
Chi-restraints excluded: chain A residue  225 GLN
Chi-restraints excluded: chain A residue  230 MET
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  445 LYS
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain A residue  587 LEU
Chi-restraints excluded: chain A residue  589 GLN
Chi-restraints excluded: chain A residue  646 SER
Chi-restraints excluded: chain A residue  688 THR
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  837 LYS
Chi-restraints excluded: chain A residue  860 ASN
Chi-restraints excluded: chain A residue  945 VAL
Chi-restraints excluded: chain B residue   48 LYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain C residue  345 LYS
Chi-restraints excluded: chain C residue  365 GLU
Chi-restraints excluded: chain C residue  379 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 88 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 94 optimal weight:    0.6980
   chunk 142 optimal weight:   50.0000
   chunk 103 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 111 optimal weight:    0.8980
   chunk 101 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
A 214 GLN
A 801 GLN
B 109 ASN
C 373 ASN
C 391 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.166849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.128120 restraints weight = 20513.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 2.01
r_work: 0.3436 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3287
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3287 r_free = 0.3287    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3287 r_free = 0.3287    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3287
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.1565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  14620  Z= 0.153
  Angle     :  0.562   9.268  19929  Z= 0.298
  Chirality :  0.042   0.264   2208
  Planarity :  0.004   0.052   2391
  Dihedral  : 15.106 137.140   2277
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.79 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.11 %
    Favored  : 81.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.21), residues: 1634
  helix:  1.66 (0.22), residues: 587
  sheet:  0.50 (0.28), residues: 344
  loop : -1.30 (0.22), residues: 703

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 470 
 HIS   0.006   0.001   HIS A 839 
 PHE   0.013   0.001   PHE A 838 
 TYR   0.021   0.001   TYR B  11 
 ARG   0.003   0.000   ARG A  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04658 (  612)
  hydrogen bonds       : angle       4.30197 ( 1715)
  covalent geometry    : bond        0.00358 (14618)
  covalent geometry    : angle       0.56169 (19929)
  Misc. bond           : bond        0.00037 (    2)

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

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

  3268 Ramachandran restraints generated.
    1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3268 Ramachandran restraints generated.
    1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  364 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 329
  time to evaluate  : 1.507 
Fit side-chains
REVERT: A  225 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8560 (mt0)
REVERT: A  291 LYS cc_start: 0.8227 (mmtm) cc_final: 0.7985 (mmtm)
REVERT: A  341 LEU cc_start: 0.8951 (mt) cc_final: 0.8739 (mt)
REVERT: A  351 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8633 (tttm)
REVERT: A  373 ASP cc_start: 0.7964 (t0) cc_final: 0.7588 (t0)
REVERT: A  413 ASN cc_start: 0.7793 (t0) cc_final: 0.7460 (t0)
REVERT: A  742 ARG cc_start: 0.7902 (ttm-80) cc_final: 0.7650 (ttm-80)
REVERT: A  842 MET cc_start: 0.8674 (mmp) cc_final: 0.8376 (mmm)
REVERT: B   96 ILE cc_start: 0.8094 (tp) cc_final: 0.7764 (tp)
REVERT: B  205 ASP cc_start: 0.8075 (t0) cc_final: 0.7673 (t0)
REVERT: C   21 ARG cc_start: 0.7756 (ptm160) cc_final: 0.7442 (ptm160)
REVERT: C   32 ASN cc_start: 0.8086 (m-40) cc_final: 0.7797 (m-40)
REVERT: C   95 MET cc_start: 0.3435 (mmp) cc_final: 0.2430 (mmp)
REVERT: C  160 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7036 (tm)
REVERT: C  184 MET cc_start: 0.8456 (mmp) cc_final: 0.8034 (mmp)
REVERT: C  224 LYS cc_start: 0.7734 (ptpp) cc_final: 0.7439 (ptpp)
REVERT: C  336 ASP cc_start: 0.8095 (m-30) cc_final: 0.7728 (m-30)
REVERT: C  395 LEU cc_start: 0.7612 (mp) cc_final: 0.7285 (mt)
REVERT: C  422 LYS cc_start: 0.8125 (tptp) cc_final: 0.7772 (tptp)
  outliers start: 35
  outliers final: 24
  residues processed: 339
  average time/residue: 1.2671
  time to fit residues: 470.8813
Evaluate side-chains
  351 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 324
  time to evaluate  : 1.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 GLU
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  143 ASP
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  215 GLU
Chi-restraints excluded: chain A residue  225 GLN
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  480 ASP
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain A residue  589 GLN
Chi-restraints excluded: chain A residue  646 SER
Chi-restraints excluded: chain A residue  688 THR
Chi-restraints excluded: chain A residue  790 GLU
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  860 ASN
Chi-restraints excluded: chain A residue  945 VAL
Chi-restraints excluded: chain B residue   48 LYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  345 LYS
Chi-restraints excluded: chain C residue  365 GLU
Chi-restraints excluded: chain C residue  379 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 132 optimal weight:   40.0000
   chunk 10 optimal weight:    0.1980
   chunk 119 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 80 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 102 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 162 optimal weight:    2.9990
   chunk 99 optimal weight:    4.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
A 709 ASN
A 801 GLN
B  59 ASN
C 373 ASN
C 397 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.166648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.127444 restraints weight = 25935.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 2.28
r_work: 0.3411 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3251
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3251 r_free = 0.3251    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3251 r_free = 0.3251    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3251
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  14620  Z= 0.163
  Angle     :  0.574  10.174  19929  Z= 0.304
  Chirality :  0.043   0.370   2208
  Planarity :  0.004   0.051   2391
  Dihedral  : 15.234 137.052   2277
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.16 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 16.83 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.21), residues: 1634
  helix:  1.68 (0.22), residues: 587
  sheet:  0.46 (0.28), residues: 350
  loop : -1.31 (0.22), residues: 697

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 470 
 HIS   0.006   0.001   HIS A 839 
 PHE   0.013   0.001   PHE A 838 
 TYR   0.025   0.001   TYR B  11 
 ARG   0.003   0.000   ARG A  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04812 (  612)
  hydrogen bonds       : angle       4.29180 ( 1715)
  covalent geometry    : bond        0.00383 (14618)
  covalent geometry    : angle       0.57431 (19929)
  Misc. bond           : bond        0.00039 (    2)

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

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

  3268 Ramachandran restraints generated.
    1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3268 Ramachandran restraints generated.
    1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  371 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 333
  time to evaluate  : 1.516 
Fit side-chains
REVERT: A  225 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8593 (mt0)
REVERT: A  291 LYS cc_start: 0.8244 (mmtm) cc_final: 0.8006 (mmtm)
REVERT: A  373 ASP cc_start: 0.8030 (t0) cc_final: 0.7636 (t0)
REVERT: A  413 ASN cc_start: 0.7814 (t0) cc_final: 0.7439 (t0)
REVERT: A  540 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8256 (mtt)
REVERT: A  742 ARG cc_start: 0.8000 (ttm-80) cc_final: 0.7750 (ttm-80)
REVERT: B   96 ILE cc_start: 0.8101 (tp) cc_final: 0.7780 (tp)
REVERT: B  205 ASP cc_start: 0.8155 (t0) cc_final: 0.7744 (t0)
REVERT: C   32 ASN cc_start: 0.8089 (m-40) cc_final: 0.7837 (m-40)
REVERT: C   95 MET cc_start: 0.3627 (mmp) cc_final: 0.2585 (mmp)
REVERT: C  160 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7059 (tm)
REVERT: C  184 MET cc_start: 0.8465 (mmp) cc_final: 0.8052 (mmp)
REVERT: C  224 LYS cc_start: 0.7696 (ptpp) cc_final: 0.7419 (ptpp)
REVERT: C  336 ASP cc_start: 0.8171 (m-30) cc_final: 0.7790 (m-30)
REVERT: C  374 ASN cc_start: 0.7167 (p0) cc_final: 0.6745 (p0)
REVERT: C  397 ASN cc_start: 0.7974 (t0) cc_final: 0.7717 (t0)
REVERT: C  422 LYS cc_start: 0.8186 (tptp) cc_final: 0.7821 (tptp)
  outliers start: 38
  outliers final: 24
  residues processed: 341
  average time/residue: 1.1887
  time to fit residues: 445.1507
Evaluate side-chains
  353 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 326
  time to evaluate  : 1.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  143 ASP
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  215 GLU
Chi-restraints excluded: chain A residue  225 GLN
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  480 ASP
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain A residue  540 MET
Chi-restraints excluded: chain A residue  646 SER
Chi-restraints excluded: chain A residue  688 THR
Chi-restraints excluded: chain A residue  764 VAL
Chi-restraints excluded: chain A residue  790 GLU
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  860 ASN
Chi-restraints excluded: chain A residue  945 VAL
Chi-restraints excluded: chain B residue   48 LYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain C residue   22 PHE
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  345 LYS
Chi-restraints excluded: chain C residue  365 GLU
Chi-restraints excluded: chain C residue  379 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 107 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 159 optimal weight:    4.9990
   chunk 51 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 108 optimal weight:    0.5980
   chunk 118 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
A 214 GLN
A 709 ASN
A 801 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.167076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.128363 restraints weight = 20495.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 2.01
r_work: 0.3442 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3290
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3290 r_free = 0.3290    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3290 r_free = 0.3290    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3290
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  14620  Z= 0.156
  Angle     :  0.576  10.292  19929  Z= 0.303
  Chirality :  0.043   0.384   2208
  Planarity :  0.004   0.052   2391
  Dihedral  : 15.252 137.116   2277
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.86 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 17.43 %
    Favored  : 80.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.21), residues: 1634
  helix:  1.68 (0.22), residues: 587
  sheet:  0.39 (0.27), residues: 356
  loop : -1.30 (0.22), residues: 691

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 470 
 HIS   0.006   0.001   HIS A 839 
 PHE   0.013   0.001   PHE A 838 
 TYR   0.026   0.001   TYR B  11 
 ARG   0.003   0.000   ARG A  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04644 (  612)
  hydrogen bonds       : angle       4.28554 ( 1715)
  covalent geometry    : bond        0.00365 (14618)
  covalent geometry    : angle       0.57613 (19929)
  Misc. bond           : bond        0.00034 (    2)

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

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

  3268 Ramachandran restraints generated.
    1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3268 Ramachandran restraints generated.
    1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  364 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 329
  time to evaluate  : 1.709 
Fit side-chains
REVERT: A  225 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8549 (mt0)
REVERT: A  291 LYS cc_start: 0.8236 (mmtm) cc_final: 0.7990 (mmtm)
REVERT: A  351 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8616 (tttm)
REVERT: A  373 ASP cc_start: 0.7982 (t0) cc_final: 0.7573 (t0)
REVERT: A  413 ASN cc_start: 0.7777 (t0) cc_final: 0.7406 (t0)
REVERT: A  540 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8193 (mtt)
REVERT: A  742 ARG cc_start: 0.7921 (ttm-80) cc_final: 0.7677 (ttm-80)
REVERT: A  792 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7952 (mm-30)
REVERT: B   96 ILE cc_start: 0.8088 (tp) cc_final: 0.7769 (tp)
REVERT: B  205 ASP cc_start: 0.8103 (t0) cc_final: 0.7696 (t0)
REVERT: C  160 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.7070 (tm)
REVERT: C  184 MET cc_start: 0.8422 (mmp) cc_final: 0.8014 (mmp)
REVERT: C  224 LYS cc_start: 0.7731 (ptpp) cc_final: 0.7450 (ptpp)
REVERT: C  336 ASP cc_start: 0.8205 (m-30) cc_final: 0.7801 (m-30)
REVERT: C  374 ASN cc_start: 0.7167 (p0) cc_final: 0.6875 (p0)
REVERT: C  422 LYS cc_start: 0.8146 (tptp) cc_final: 0.7789 (tptp)
  outliers start: 35
  outliers final: 24
  residues processed: 338
  average time/residue: 1.2666
  time to fit residues: 470.8789
Evaluate side-chains
  347 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 319
  time to evaluate  : 1.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  143 ASP
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  215 GLU
Chi-restraints excluded: chain A residue  225 GLN
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  445 LYS
Chi-restraints excluded: chain A residue  480 ASP
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain A residue  540 MET
Chi-restraints excluded: chain A residue  589 GLN
Chi-restraints excluded: chain A residue  646 SER
Chi-restraints excluded: chain A residue  688 THR
Chi-restraints excluded: chain A residue  764 VAL
Chi-restraints excluded: chain A residue  790 GLU
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  860 ASN
Chi-restraints excluded: chain A residue  945 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain C residue   22 PHE
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  345 LYS
Chi-restraints excluded: chain C residue  365 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 99 optimal weight:    5.9990
   chunk 114 optimal weight:    1.9990
   chunk 133 optimal weight:   30.0000
   chunk 70 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 140 optimal weight:    7.9990
   chunk 48 optimal weight:    0.6980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 136 ASN
A 204 ASN
A 214 GLN
A 709 ASN
A 801 GLN
C 397 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.166470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.127483 restraints weight = 24840.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 2.47
r_work: 0.3400 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3237
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3237 r_free = 0.3237    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3237
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.1671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  14620  Z= 0.184
  Angle     :  0.607  10.793  19929  Z= 0.320
  Chirality :  0.044   0.410   2208
  Planarity :  0.004   0.052   2391
  Dihedral  : 15.333 136.472   2277
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.47 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 17.95 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.21), residues: 1634
  helix:  1.62 (0.22), residues: 587
  sheet:  0.54 (0.27), residues: 355
  loop : -1.39 (0.22), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 470 
 HIS   0.006   0.001   HIS A 839 
 PHE   0.013   0.001   PHE A 838 
 TYR   0.026   0.001   TYR B  11 
 ARG   0.003   0.000   ARG A  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05084 (  612)
  hydrogen bonds       : angle       4.33360 ( 1715)
  covalent geometry    : bond        0.00439 (14618)
  covalent geometry    : angle       0.60666 (19929)
  Misc. bond           : bond        0.00065 (    2)

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

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

  3268 Ramachandran restraints generated.
    1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3268 Ramachandran restraints generated.
    1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  365 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 332
  time to evaluate  : 1.678 
Fit side-chains
REVERT: A  225 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8608 (mt0)
REVERT: A  291 LYS cc_start: 0.8268 (mmtm) cc_final: 0.8023 (mmtm)
REVERT: A  351 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8651 (tttm)
REVERT: A  373 ASP cc_start: 0.8050 (t0) cc_final: 0.7657 (t0)
REVERT: A  413 ASN cc_start: 0.7812 (t0) cc_final: 0.7434 (t0)
REVERT: A  540 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8315 (mtt)
REVERT: A  742 ARG cc_start: 0.8012 (ttm-80) cc_final: 0.7767 (ttm-80)
REVERT: A  792 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8033 (mm-30)
REVERT: A  842 MET cc_start: 0.8727 (mmp) cc_final: 0.8443 (mmm)
REVERT: B   96 ILE cc_start: 0.8136 (tp) cc_final: 0.7815 (tp)
REVERT: B  205 ASP cc_start: 0.8205 (t0) cc_final: 0.7794 (t0)
REVERT: C    9 ASN cc_start: 0.8051 (OUTLIER) cc_final: 0.7599 (m-40)
REVERT: C  184 MET cc_start: 0.8486 (mmp) cc_final: 0.8084 (mmp)
REVERT: C  224 LYS cc_start: 0.7682 (ptpp) cc_final: 0.7405 (ptpp)
REVERT: C  336 ASP cc_start: 0.8245 (m-30) cc_final: 0.7821 (m-30)
REVERT: C  395 LEU cc_start: 0.7526 (mp) cc_final: 0.6962 (mt)
REVERT: C  422 LYS cc_start: 0.8242 (tptp) cc_final: 0.7887 (tptp)
  outliers start: 33
  outliers final: 25
  residues processed: 339
  average time/residue: 1.2373
  time to fit residues: 460.2256
Evaluate side-chains
  356 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 327
  time to evaluate  : 1.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  143 ASP
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  215 GLU
Chi-restraints excluded: chain A residue  225 GLN
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  445 LYS
Chi-restraints excluded: chain A residue  480 ASP
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain A residue  540 MET
Chi-restraints excluded: chain A residue  589 GLN
Chi-restraints excluded: chain A residue  646 SER
Chi-restraints excluded: chain A residue  688 THR
Chi-restraints excluded: chain A residue  764 VAL
Chi-restraints excluded: chain A residue  790 GLU
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  860 ASN
Chi-restraints excluded: chain A residue  945 VAL
Chi-restraints excluded: chain B residue   48 LYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain C residue    9 ASN
Chi-restraints excluded: chain C residue   22 PHE
Chi-restraints excluded: chain C residue  345 LYS
Chi-restraints excluded: chain C residue  365 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 152 optimal weight:    0.0770
   chunk 94 optimal weight:    2.9990
   chunk 127 optimal weight:    0.1980
   chunk 30 optimal weight:    2.9990
   chunk 133 optimal weight:   50.0000
   chunk 106 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 108 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.0342

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
A 709 ASN
A 801 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.166361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.126675 restraints weight = 21204.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 2.21
r_work: 0.3401 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3238
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3238
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.1696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  14620  Z= 0.186
  Angle     :  0.609  10.699  19929  Z= 0.321
  Chirality :  0.044   0.417   2208
  Planarity :  0.004   0.052   2391
  Dihedral  : 15.366 136.715   2277
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.10 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 17.95 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.21), residues: 1634
  helix:  1.64 (0.22), residues: 584
  sheet:  0.37 (0.27), residues: 356
  loop : -1.36 (0.22), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 470 
 HIS   0.006   0.001   HIS A 839 
 PHE   0.013   0.001   PHE A 838 
 TYR   0.027   0.001   TYR B  11 
 ARG   0.003   0.000   ARG A  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05055 (  612)
  hydrogen bonds       : angle       4.34328 ( 1715)
  covalent geometry    : bond        0.00445 (14618)
  covalent geometry    : angle       0.60908 (19929)
  Misc. bond           : bond        0.00056 (    2)

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

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

  3268 Ramachandran restraints generated.
    1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3268 Ramachandran restraints generated.
    1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  366 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 332
  time to evaluate  : 1.680 
Fit side-chains
REVERT: A  225 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8594 (mt0)
REVERT: A  291 LYS cc_start: 0.8274 (mmtm) cc_final: 0.8034 (mmtm)
REVERT: A  351 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8656 (tttm)
REVERT: A  373 ASP cc_start: 0.8051 (t0) cc_final: 0.7662 (t0)
REVERT: A  413 ASN cc_start: 0.7800 (t0) cc_final: 0.7405 (t0)
REVERT: A  540 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8305 (mtt)
REVERT: A  742 ARG cc_start: 0.8011 (ttm-80) cc_final: 0.7761 (ttm-80)
REVERT: A  792 GLU cc_start: 0.8284 (mm-30) cc_final: 0.8048 (mm-30)
REVERT: A  842 MET cc_start: 0.8721 (mmp) cc_final: 0.8433 (mmm)
REVERT: B   96 ILE cc_start: 0.8152 (tp) cc_final: 0.7831 (tp)
REVERT: B  205 ASP cc_start: 0.8210 (t0) cc_final: 0.7800 (t0)
REVERT: C    9 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7559 (m-40)
REVERT: C   95 MET cc_start: 0.3375 (mmp) cc_final: 0.3097 (mmp)
REVERT: C  184 MET cc_start: 0.8448 (mmp) cc_final: 0.8041 (mmp)
REVERT: C  224 LYS cc_start: 0.7701 (ptpp) cc_final: 0.7422 (ptpp)
REVERT: C  336 ASP cc_start: 0.8238 (m-30) cc_final: 0.7820 (m-30)
REVERT: C  374 ASN cc_start: 0.7333 (p0) cc_final: 0.6973 (p0)
REVERT: C  395 LEU cc_start: 0.7472 (mp) cc_final: 0.6869 (mt)
REVERT: C  422 LYS cc_start: 0.8240 (tptp) cc_final: 0.7892 (tptp)
  outliers start: 34
  outliers final: 26
  residues processed: 341
  average time/residue: 1.2045
  time to fit residues: 450.3452
Evaluate side-chains
  357 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 327
  time to evaluate  : 1.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  143 ASP
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  215 GLU
Chi-restraints excluded: chain A residue  225 GLN
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  445 LYS
Chi-restraints excluded: chain A residue  480 ASP
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain A residue  540 MET
Chi-restraints excluded: chain A residue  589 GLN
Chi-restraints excluded: chain A residue  646 SER
Chi-restraints excluded: chain A residue  688 THR
Chi-restraints excluded: chain A residue  764 VAL
Chi-restraints excluded: chain A residue  790 GLU
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  860 ASN
Chi-restraints excluded: chain A residue  945 VAL
Chi-restraints excluded: chain B residue   48 LYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  130 THR
Chi-restraints excluded: chain B residue  191 LYS
Chi-restraints excluded: chain C residue    9 ASN
Chi-restraints excluded: chain C residue   22 PHE
Chi-restraints excluded: chain C residue  345 LYS
Chi-restraints excluded: chain C residue  365 GLU
Chi-restraints excluded: chain C residue  379 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 120 optimal weight:    0.3980
   chunk 38 optimal weight:    1.9990
   chunk 152 optimal weight:    0.3980
   chunk 140 optimal weight:    8.9990
   chunk 113 optimal weight:    2.9990
   chunk 131 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9990
   chunk 107 optimal weight:    0.7980
   chunk 155 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
A 214 GLN
A 709 ASN
A 801 GLN
C  94 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.167526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.128502 restraints weight = 20621.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 2.04
r_work: 0.3439 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3290 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3288
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3288 r_free = 0.3288    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3288 r_free = 0.3288    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3288
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  14620  Z= 0.147
  Angle     :  0.591  10.554  19929  Z= 0.310
  Chirality :  0.043   0.409   2208
  Planarity :  0.004   0.052   2391
  Dihedral  : 15.306 137.047   2277
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.98 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 18.55 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.21), residues: 1634
  helix:  1.71 (0.22), residues: 583
  sheet:  0.37 (0.27), residues: 356
  loop : -1.34 (0.22), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 470 
 HIS   0.006   0.001   HIS A 839 
 PHE   0.013   0.001   PHE A 992 
 TYR   0.027   0.001   TYR B  11 
 ARG   0.003   0.000   ARG A 577 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04494 (  612)
  hydrogen bonds       : angle       4.28589 ( 1715)
  covalent geometry    : bond        0.00342 (14618)
  covalent geometry    : angle       0.59142 (19929)
  Misc. bond           : bond        0.00047 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 16302.20 seconds
wall clock time: 279 minutes 55.08 seconds (16795.08 seconds total)