Starting phenix.real_space_refine
on Thu Jul 31 20:02:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zgq_14711/07_2025/7zgq_14711.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zgq_14711/07_2025/7zgq_14711.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zgq_14711/07_2025/7zgq_14711.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zgq_14711/07_2025/7zgq_14711.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zgq_14711/07_2025/7zgq_14711.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zgq_14711/07_2025/7zgq_14711.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      68      5.16       5
     C    8771      2.51       5
     N    2310      2.21       5
     O    2555      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13704
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 285
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 285
          Classifications: {'peptide': 38}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 33}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 9691
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1237, 9691
          Classifications: {'peptide': 1237}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 51, 'TRANS': 1185}
          Chain breaks: 8
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 177
          Unresolved non-hydrogen angles: 201
          Unresolved non-hydrogen dihedrals: 154
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 92
    Chain: "B"
      Number of atoms: 705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 705
          Classifications: {'peptide': 90}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 11, 'TRANS': 78}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 64
          Unresolved non-hydrogen dihedrals: 50
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 31
    Chain: "D"
      Number of atoms: 3023
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 3023
          Classifications: {'peptide': 384}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 19, 'TRANS': 364}
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 109
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 58
  Time building chain proxies: 8.53, per 1000 atoms: 0.62
  Number of scatterers: 13704
  At special positions: 0
  Unit cell: (110.55, 108.9, 114.675, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      68     16.00
     O    2555      8.00
     N    2310      7.00
     C    8771      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.09
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3446 Ramachandran restraints generated.
    1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3332

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 28 sheets defined
      8.8% alpha, 32.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 105 through 112
      removed outlier: 3.687A  pdb=" N   LYS A 112 " --> pdb=" O   LYS A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 702
      removed outlier: 3.853A  pdb=" N   GLU A 701 " --> pdb=" O   GLU A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 840 through 844
    Processing helix  chain 'A' and resid 1203 through 1207
      removed outlier: 4.110A  pdb=" N   LEU A1207 " --> pdb=" O   PRO A1204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1262 through 1280
    Processing helix  chain 'A' and resid 1287 through 1293
    Processing helix  chain 'A' and resid 1297 through 1301
      removed outlier: 4.135A  pdb=" N   GLY A1301 " --> pdb=" O   TYR A1298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1310 through 1315
      removed outlier: 3.547A  pdb=" N   ARG A1315 " --> pdb=" O   ASN A1311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1320 through 1329
      removed outlier: 3.505A  pdb=" N   GLN A1329 " --> pdb=" O   LYS A1325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1334 through 1348
      removed outlier: 3.632A  pdb=" N   GLU A1338 " --> pdb=" O   HIS A1334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1349 through 1355
      removed outlier: 4.084A  pdb=" N   SER A1352 " --> pdb=" O   SER A1349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 15 through 22
    Processing helix  chain 'B' and resid 58 through 63
      removed outlier: 3.890A  pdb=" N   ASN B  63 " --> pdb=" O   ILE B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 72
    Processing helix  chain 'B' and resid 88 through 92
      removed outlier: 3.655A  pdb=" N   LYS B  91 " --> pdb=" O   ASN B  88 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   MET B  92 " --> pdb=" O   LEU B  89 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 88 through 92'
    Processing helix  chain 'D' and resid 35 through 48
    Processing helix  chain 'D' and resid 58 through 65
      removed outlier: 3.613A  pdb=" N   ILE D  63 " --> pdb=" O   SER D  60 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 71
    Processing helix  chain 'D' and resid 72 through 80
      removed outlier: 3.975A  pdb=" N   ASP D  75 " --> pdb=" O   ARG D  72 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   VAL D  77 " --> pdb=" O   ARG D  74 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 525 through 526
      removed outlier: 6.619A  pdb=" N   ILE A  87 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   LEU A 102 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   ILE A  85 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LYS A  84 " --> pdb=" O   THR A  80 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   THR A  80 " --> pdb=" O   LYS A  84 " (cutoff:3.500A)
      removed outlier: 5.779A  pdb=" N   PHE A  90 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
      removed outlier: 8.164A  pdb=" N   SER A  74 " --> pdb=" O   PHE A  90 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 546 through 547
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1224 through 1231
      removed outlier: 3.827A  pdb=" N   CYS A1226 " --> pdb=" O   GLY A1249 " (cutoff:3.500A)
      removed outlier: 7.448A  pdb=" N   PHE A1244 " --> pdb=" O   PRO A1260 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 15 through 19
      removed outlier: 6.140A  pdb=" N   ARG A  41 " --> pdb=" O   LEU A  50 " (cutoff:3.500A)
      removed outlier: 5.826A  pdb=" N   LEU A  50 " --> pdb=" O   ARG A  41 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 122 through 125
    Processing sheet with id=AA6, first strand: chain 'A' and resid 213 through 218
      removed outlier: 6.695A  pdb=" N   LEU A 230 " --> pdb=" O   ILE A 214 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   ILE A 216 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ALA A 228 " --> pdb=" O   ILE A 216 " (cutoff:3.500A)
      removed outlier: 4.838A  pdb=" N   PHE A 218 " --> pdb=" O   THR A 226 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   THR A 226 " --> pdb=" O   PHE A 218 " (cutoff:3.500A)
      removed outlier: 4.794A  pdb=" N   THR A 248 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
      removed outlier: 5.264A  pdb=" N   LYS A 275 " --> pdb=" O   THR A 248 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   TYR A 250 " --> pdb=" O   PHE A 273 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   PHE A 273 " --> pdb=" O   TYR A 250 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   ILE A 252 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 281 through 286
      removed outlier: 4.180A  pdb=" N   GLU A 298 " --> pdb=" O   GLY A 295 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   SER A 310 " --> pdb=" O   PHE A 301 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   ASP A 303 " --> pdb=" O   LEU A 308 " (cutoff:3.500A)
      removed outlier: 7.129A  pdb=" N   LEU A 308 " --> pdb=" O   ASP A 303 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   GLN A 309 " --> pdb=" O   ILE A 327 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   ASN A 329 " --> pdb=" O   GLN A 309 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   THR A 311 " --> pdb=" O   ASN A 329 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 344 through 347
      removed outlier: 3.945A  pdb=" N   LEU A 363 " --> pdb=" O   ILE A 375 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLN A 376 " --> pdb=" O   ASP A 388 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   ASP A 388 " --> pdb=" O   GLN A 376 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   GLU A 378 " --> pdb=" O   LYS A 386 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   LYS A 386 " --> pdb=" O   GLU A 378 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 405 through 410
      removed outlier: 3.721A  pdb=" N   CYS A 407 " --> pdb=" O   GLY A 425 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ALA A 431 " --> pdb=" O   SER A 504 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   SER A 504 " --> pdb=" O   ALA A 431 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   VAL A 433 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLU A 500 " --> pdb=" O   ARG A 435 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 513 through 517
      removed outlier: 4.193A  pdb=" N   SER A 513 " --> pdb=" O   THR A 542 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 525 through 526
    Processing sheet with id=AB3, first strand: chain 'A' and resid 561 through 564
      removed outlier: 5.658A  pdb=" N   ILE A 562 " --> pdb=" O   THR A 915 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   THR A 915 " --> pdb=" O   ILE A 562 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   LEU A 564 " --> pdb=" O   VAL A 913 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 574 through 577
      removed outlier: 4.983A  pdb=" N   TYR A 585 " --> pdb=" O   LEU A 577 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 621 through 625
      removed outlier: 3.618A  pdb=" N   THR A 650 " --> pdb=" O   LEU A 641 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 658 through 663
    Processing sheet with id=AB7, first strand: chain 'A' and resid 704 through 712
      removed outlier: 3.599A  pdb=" N   SER A 706 " --> pdb=" O   VAL A 735 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   PHE A 744 " --> pdb=" O   PHE A 732 " (cutoff:3.500A)
      removed outlier: 5.059A  pdb=" N   ILE A 741 " --> pdb=" O   LEU A 755 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   TYR A 766 " --> pdb=" O   ASN A 756 " (cutoff:3.500A)
      removed outlier: 5.410A  pdb=" N   GLU A 797 " --> pdb=" O   LYS A 813 " (cutoff:3.500A)
      removed outlier: 5.674A  pdb=" N   GLU A 796 " --> pdb=" O   LYS A 789 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   LYS A 789 " --> pdb=" O   GLU A 796 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   TYR A 798 " --> pdb=" O   ILE A 787 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   ILE A 787 " --> pdb=" O   TYR A 798 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   THR A 800 " --> pdb=" O   VAL A 785 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   VAL A 785 " --> pdb=" O   THR A 800 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   LEU A 802 " --> pdb=" O   LYS A 783 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 851 through 854
    Processing sheet with id=AB9, first strand: chain 'A' and resid 944 through 950
      removed outlier: 6.592A  pdb=" N   LEU A 944 " --> pdb=" O   CYS A 961 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   CYS A 961 " --> pdb=" O   LEU A 944 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   LYS A 946 " --> pdb=" O   SER A 959 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   SER A 959 " --> pdb=" O   LYS A 946 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   TYR A 960 " --> pdb=" O   GLY A 992 " (cutoff:3.500A)
      removed outlier: 7.466A  pdb=" N   SER A 991 " --> pdb=" O   ASP A1008 " (cutoff:3.500A)
      removed outlier: 5.369A  pdb=" N   ASP A1008 " --> pdb=" O   SER A 991 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   ILE A 993 " --> pdb=" O   LYS A1006 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   LYS A1006 " --> pdb=" O   ILE A 993 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   LEU A 995 " --> pdb=" O   ILE A1004 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 1013 through 1023
      removed outlier: 6.704A  pdb=" N   GLY A1039 " --> pdb=" O   ASN A1016 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   MET A1018 " --> pdb=" O   ILE A1037 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   ILE A1037 " --> pdb=" O   MET A1018 " (cutoff:3.500A)
      removed outlier: 4.616A  pdb=" N   SER A1020 " --> pdb=" O   TYR A1035 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   TYR A1035 " --> pdb=" O   SER A1020 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   MET A1022 " --> pdb=" O   ARG A1033 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   ARG A1033 " --> pdb=" O   MET A1022 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   GLU A1034 " --> pdb=" O   VAL A1059 " (cutoff:3.500A)
      removed outlier: 5.276A  pdb=" N   VAL A1059 " --> pdb=" O   GLU A1034 " (cutoff:3.500A)
      removed outlier: 5.164A  pdb=" N   THR A1051 " --> pdb=" O   ASN A1042 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   GLY A1052 " --> pdb=" O   GLU A1082 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   GLU A1082 " --> pdb=" O   GLY A1052 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   PHE A1054 " --> pdb=" O   GLN A1080 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   GLN A1080 " --> pdb=" O   PHE A1054 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   ILE A1056 " --> pdb=" O   ILE A1078 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 1090 through 1093
      removed outlier: 6.568A  pdb=" N   VAL A1105 " --> pdb=" O   PHE A1121 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   PHE A1121 " --> pdb=" O   VAL A1105 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   VAL A1107 " --> pdb=" O   VAL A1119 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ILE A1117 " --> pdb=" O   ASP A1109 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'A' and resid 1128 through 1134
      removed outlier: 4.214A  pdb=" N   ASP A1130 " --> pdb=" O   GLY A1141 " (cutoff:3.500A)
      removed outlier: 5.610A  pdb=" N   PHE A1147 " --> pdb=" O   SER A1165 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   GLY A1151 " --> pdb=" O   SER A1161 " (cutoff:3.500A)
      removed outlier: 5.454A  pdb=" N   SER A1161 " --> pdb=" O   GLY A1151 " (cutoff:3.500A)
      removed outlier: 7.812A  pdb=" N   ASP A1153 " --> pdb=" O   MET A1159 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   MET A1159 " --> pdb=" O   ASP A1153 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   LEU A1212 " --> pdb=" O   LEU A1162 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   ARG A1164 " --> pdb=" O   LEU A1212 " (cutoff:3.500A)
      removed outlier: 7.567A  pdb=" N   HIS A1214 " --> pdb=" O   ARG A1164 " (cutoff:3.500A)
      removed outlier: 5.962A  pdb=" N   HIS A1214 " --> pdb=" O   LYS A1198 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   LYS A1198 " --> pdb=" O   HIS A1214 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   ASN A1193 " --> pdb=" O   ASP A1189 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   TYR A1184 " --> pdb=" O   PHE A1176 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   PHE A1176 " --> pdb=" O   TYR A1184 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   ALA A1186 " --> pdb=" O   LEU A1174 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   LEU A1174 " --> pdb=" O   ALA A1186 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   THR A1188 " --> pdb=" O   MET A1172 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'D' and resid 83 through 88
      removed outlier: 5.340A  pdb=" N   PHE D  84 " --> pdb=" O   THR D 378 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   THR D 378 " --> pdb=" O   PHE D  84 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   HIS D  86 " --> pdb=" O   PHE D 376 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'D' and resid 99 through 101
    Processing sheet with id=AC6, first strand: chain 'D' and resid 138 through 143
      removed outlier: 3.614A  pdb=" N   THR D 140 " --> pdb=" O   GLY D 153 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'D' and resid 180 through 185
      removed outlier: 4.362A  pdb=" N   SER D 196 " --> pdb=" O   ILE D 200 " (cutoff:3.500A)
      removed outlier: 5.687A  pdb=" N   ILE D 200 " --> pdb=" O   SER D 196 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU D 201 " --> pdb=" O   LEU D 215 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   ARG D 213 " --> pdb=" O   ILE D 203 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   ASN D 205 " --> pdb=" O   GLN D 211 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   GLN D 211 " --> pdb=" O   ASN D 205 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'D' and resid 224 through 227
      removed outlier: 3.622A  pdb=" N   ILE D 234 " --> pdb=" O   TRP D 246 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'D' and resid 264 through 269
      removed outlier: 3.532A  pdb=" N   LYS D 266 " --> pdb=" O   ILE D 280 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   SER D 285 " --> pdb=" O   SER D 281 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   CYS D 286 " --> pdb=" O   CYS D 300 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   CYS D 300 " --> pdb=" O   CYS D 286 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   VAL D 288 " --> pdb=" O   LEU D 298 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'D' and resid 307 through 312
      removed outlier: 6.768A  pdb=" N   ALA D 323 " --> pdb=" O   MET D 308 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   LEU D 310 " --> pdb=" O   THR D 321 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   THR D 321 " --> pdb=" O   LEU D 310 " (cutoff:3.500A)
      removed outlier: 5.109A  pdb=" N   TRP D 312 " --> pdb=" O   MET D 319 " (cutoff:3.500A)
      removed outlier: 7.709A  pdb=" N   MET D 319 " --> pdb=" O   TRP D 312 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   CYS D 324 " --> pdb=" O   SER D 328 " (cutoff:3.500A)
      removed outlier: 5.370A  pdb=" N   SER D 328 " --> pdb=" O   CYS D 324 " (cutoff:3.500A)

    405 hydrogen bonds defined for protein.
    1044 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 6.54

  Time building geometry restraints manager: 3.74 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4325
        1.34 -     1.45: 2030
        1.45 -     1.57: 7540
        1.57 -     1.69: 0
        1.69 -     1.81: 111
  Bond restraints: 14006
  Sorted by residual:
  bond pdb=" N   ILE C 526 "
       pdb=" CA  ILE C 526 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.27e-02 6.20e+03 7.68e+00
  bond pdb=" N   GLN C 527 "
       pdb=" CA  GLN C 527 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.033 1.41e-02 5.03e+03 5.34e+00
  bond pdb=" C   ALA A 196 "
       pdb=" N   PRO A 197 "
    ideal  model  delta    sigma   weight residual
    1.330  1.355 -0.025 1.25e-02 6.40e+03 3.99e+00
  bond pdb=" N   LEU A 392 "
       pdb=" CA  LEU A 392 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.56e-02 4.11e+03 3.42e+00
  bond pdb=" N   SER C 529 "
       pdb=" CA  SER C 529 "
    ideal  model  delta    sigma   weight residual
    1.462  1.487 -0.025 1.38e-02 5.25e+03 3.32e+00
  ... (remaining 14001 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 18745
        1.83 -     3.67: 229
        3.67 -     5.50: 35
        5.50 -     7.34: 5
        7.34 -     9.17: 5
  Bond angle restraints: 19019
  Sorted by residual:
  angle pdb=" N   ILE A 511 "
        pdb=" CA  ILE A 511 "
        pdb=" C   ILE A 511 "
      ideal   model   delta    sigma   weight residual
     108.54   99.63    8.91 1.48e+00 4.57e-01 3.62e+01
  angle pdb=" C   ILE A 511 "
        pdb=" CA  ILE A 511 "
        pdb=" CB  ILE A 511 "
      ideal   model   delta    sigma   weight residual
     111.08  117.70   -6.62 1.17e+00 7.31e-01 3.20e+01
  angle pdb=" N   THR A 512 "
        pdb=" CA  THR A 512 "
        pdb=" C   THR A 512 "
      ideal   model   delta    sigma   weight residual
     113.97  108.62    5.35 1.28e+00 6.10e-01 1.75e+01
  angle pdb=" CA  SER C 529 "
        pdb=" C   SER C 529 "
        pdb=" O   SER C 529 "
      ideal   model   delta    sigma   weight residual
     122.13  118.03    4.10 1.13e+00 7.83e-01 1.32e+01
  angle pdb=" CA  PRO B  43 "
        pdb=" N   PRO B  43 "
        pdb=" CD  PRO B  43 "
      ideal   model   delta    sigma   weight residual
     112.00  107.33    4.67 1.40e+00 5.10e-01 1.11e+01
  ... (remaining 19014 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 7284
       17.47 -    34.95: 845
       34.95 -    52.42: 238
       52.42 -    69.89: 41
       69.89 -    87.37: 11
  Dihedral angle restraints: 8419
    sinusoidal: 3284
      harmonic: 5135
  Sorted by residual:
  dihedral pdb=" CA  TRP D 220 "
           pdb=" C   TRP D 220 "
           pdb=" N   ASP D 221 "
           pdb=" CA  ASP D 221 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.19   26.81     0      5.00e+00 4.00e-02 2.88e+01
  dihedral pdb=" CA  GLU A1155 "
           pdb=" C   GLU A1155 "
           pdb=" N   PRO A1156 "
           pdb=" CA  PRO A1156 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.24   25.76     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" CA  VAL A 663 "
           pdb=" C   VAL A 663 "
           pdb=" N   MET A 664 "
           pdb=" CA  MET A 664 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.78   21.22     0      5.00e+00 4.00e-02 1.80e+01
  ... (remaining 8416 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1418
       0.036 -    0.071: 489
       0.071 -    0.107: 199
       0.107 -    0.142: 75
       0.142 -    0.178: 1
  Chirality restraints: 2182
  Sorted by residual:
  chirality pdb=" CA  ILE C 526 "
            pdb=" N   ILE C 526 "
            pdb=" C   ILE C 526 "
            pdb=" CB  ILE C 526 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.93e-01
  chirality pdb=" CA  ILE A 216 "
            pdb=" N   ILE A 216 "
            pdb=" C   ILE A 216 "
            pdb=" CB  ILE A 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.61e-01
  chirality pdb=" CA  GLU A1155 "
            pdb=" N   GLU A1155 "
            pdb=" C   GLU A1155 "
            pdb=" CB  GLU A1155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.38e-01
  ... (remaining 2179 not shown)

  Planarity restraints: 2426
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 390 "    0.026 5.00e-02 4.00e+02   3.87e-02 2.40e+00
        pdb=" N   PRO D 391 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO D 391 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 391 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP D 384 "    0.007 2.00e-02 2.50e+03   1.41e-02 1.99e+00
        pdb=" C   ASP D 384 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   ASP D 384 "    0.009 2.00e-02 2.50e+03
        pdb=" N   PRO D 385 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 137 "    0.007 2.00e-02 2.50e+03   1.39e-02 1.93e+00
        pdb=" C   ASN A 137 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   ASN A 137 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ASP A 138 "    0.008 2.00e-02 2.50e+03
  ... (remaining 2423 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 578
        2.71 -     3.26: 13058
        3.26 -     3.80: 23176
        3.80 -     4.35: 30032
        4.35 -     4.90: 50742
  Nonbonded interactions: 117586
  Sorted by model distance:
  nonbonded pdb=" N   ASP A1296 "
            pdb=" OD1 ASP A1296 "
     model   vdw
     2.162 3.120
  nonbonded pdb=" OH  TYR A1266 "
            pdb=" O   PRO A1306 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OG  SER A 520 "
            pdb=" OE1 GLU A 536 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OG1 THR A  43 "
            pdb=" OD1 ASP A  45 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O   ILE A 511 "
            pdb=" OG  SER A1225 "
     model   vdw
     2.230 3.040
  ... (remaining 117581 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.570
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     35.380
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  14006  Z= 0.128
  Angle     :  0.547   9.169  19019  Z= 0.298
  Chirality :  0.045   0.178   2182
  Planarity :  0.003   0.039   2426
  Dihedral  : 16.532  87.368   5087
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 24.57 %
    Favored  : 72.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.20), residues: 1723
  helix: -0.94 (0.49), residues: 112
  sheet:  0.31 (0.22), residues: 567
  loop : -1.37 (0.19), residues: 1044

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 312 
 HIS   0.003   0.001   HIS A 103 
 PHE   0.019   0.001   PHE C 555 
 TYR   0.024   0.001   TYR B  23 
 ARG   0.005   0.000   ARG A 612 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25425 (  405)
  hydrogen bonds       : angle       9.11745 ( 1044)
  covalent geometry    : bond        0.00271 (14006)
  covalent geometry    : angle       0.54675 (19019)

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

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

  3446 Ramachandran restraints generated.
    1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3446 Ramachandran restraints generated.
    1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 138
  time to evaluate  : 1.450 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 49
  outliers final: 43
  residues processed: 183
  average time/residue: 0.8785
  time to fit residues: 182.3371
Evaluate side-chains
  173 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 130
  time to evaluate  : 1.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  532 SER
Chi-restraints excluded: chain C residue  552 VAL
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  289 ASN
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  345 ILE
Chi-restraints excluded: chain A residue  515 THR
Chi-restraints excluded: chain A residue  522 ILE
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  608 HIS
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  636 THR
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  745 THR
Chi-restraints excluded: chain A residue  943 THR
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue  958 VAL
Chi-restraints excluded: chain A residue  983 VAL
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1014 VAL
Chi-restraints excluded: chain A residue 1021 SER
Chi-restraints excluded: chain A residue 1048 THR
Chi-restraints excluded: chain A residue 1060 ILE
Chi-restraints excluded: chain A residue 1063 VAL
Chi-restraints excluded: chain A residue 1089 THR
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1158 ARG
Chi-restraints excluded: chain A residue 1160 ILE
Chi-restraints excluded: chain A residue 1189 ASP
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1241 VAL
Chi-restraints excluded: chain A residue 1296 ASP
Chi-restraints excluded: chain B residue   78 ASN
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   88 SER
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain D residue  172 ILE
Chi-restraints excluded: chain D residue  293 TYR
Chi-restraints excluded: chain D residue  397 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 146 optimal weight:    3.9990
   chunk 131 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 44 optimal weight:    6.9990
   chunk 88 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 135 optimal weight:   10.0000
   chunk 52 optimal weight:    0.0470
   chunk 82 optimal weight:    0.7980
   chunk 100 optimal weight:    5.9990
   chunk 157 optimal weight:    0.0770
   overall best weight:    0.9840

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

Flipped N/Q/H residues before XYZ refinement:
** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 146 HIS
A 376 GLN
A 608 HIS
A 740 GLN
A 788 ASN
A1012 ASN
** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  62 GLN
D 188 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.122017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.102848 restraints weight = 24079.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 2.10
r_work: 0.3327 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3217 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.0848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14006  Z= 0.137
  Angle     :  0.559   9.623  19019  Z= 0.297
  Chirality :  0.047   0.189   2182
  Planarity :  0.004   0.072   2426
  Dihedral  :  6.655  54.510   1941
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 21.92 %
    Favored  : 72.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.20), residues: 1723
  helix: -1.05 (0.47), residues: 125
  sheet:  0.03 (0.21), residues: 581
  loop : -1.24 (0.19), residues: 1017

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 162 
 HIS   0.004   0.001   HIS A 146 
 PHE   0.015   0.001   PHE C 555 
 TYR   0.015   0.001   TYR D  43 
 ARG   0.004   0.000   ARG A 963 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04921 (  405)
  hydrogen bonds       : angle       6.57420 ( 1044)
  covalent geometry    : bond        0.00304 (14006)
  covalent geometry    : angle       0.55862 (19019)

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

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

  3446 Ramachandran restraints generated.
    1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3446 Ramachandran restraints generated.
    1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 149
  time to evaluate  : 1.533 
Fit side-chains
TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  298 GLU cc_start: 0.7201 (mp0) cc_final: 0.6992 (mp0)
REVERT: A  751 ARG cc_start: 0.7034 (mtm180) cc_final: 0.6576 (mtp85)
REVERT: B   22 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6767 (mt-10)
REVERT: D  221 ASP cc_start: 0.7052 (t0) cc_final: 0.6843 (t0)
REVERT: D  340 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8032 (pp20)
  outliers start: 79
  outliers final: 37
  residues processed: 204
  average time/residue: 0.9057
  time to fit residues: 210.3713
Evaluate side-chains
  170 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 132
  time to evaluate  : 1.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  552 VAL
Chi-restraints excluded: chain A residue   62 ASP
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  403 SER
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  515 THR
Chi-restraints excluded: chain A residue  526 VAL
Chi-restraints excluded: chain A residue  608 HIS
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  636 THR
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  788 ASN
Chi-restraints excluded: chain A residue  943 THR
Chi-restraints excluded: chain A residue  983 VAL
Chi-restraints excluded: chain A residue 1004 ILE
Chi-restraints excluded: chain A residue 1014 VAL
Chi-restraints excluded: chain A residue 1048 THR
Chi-restraints excluded: chain A residue 1063 VAL
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1183 MET
Chi-restraints excluded: chain A residue 1185 PHE
Chi-restraints excluded: chain A residue 1189 ASP
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1241 VAL
Chi-restraints excluded: chain B residue   22 GLU
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   88 SER
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain D residue  130 LEU
Chi-restraints excluded: chain D residue  254 ILE
Chi-restraints excluded: chain D residue  293 TYR
Chi-restraints excluded: chain D residue  295 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 170 optimal weight:    0.9980
   chunk 114 optimal weight:    5.9990
   chunk 43 optimal weight:    7.9990
   chunk 98 optimal weight:    0.0570
   chunk 112 optimal weight:    9.9990
   chunk 150 optimal weight:    8.9990
   chunk 6 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 166 optimal weight:    6.9990
   chunk 60 optimal weight:    9.9990
   chunk 134 optimal weight:    2.9990
   overall best weight:    2.6104

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

Flipped N/Q/H residues before XYZ refinement:
** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 660 HIS
** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1012 ASN
** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  62 GLN
D 100 GLN
D 188 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.118489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.099061 restraints weight = 24276.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 2.10
r_work: 0.3267 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3155 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.1147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  14006  Z= 0.248
  Angle     :  0.640  13.854  19019  Z= 0.336
  Chirality :  0.049   0.164   2182
  Planarity :  0.004   0.048   2426
  Dihedral  :  6.658  51.343   1905
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 21.59 %
    Favored  : 72.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.19), residues: 1723
  helix: -0.87 (0.48), residues: 118
  sheet: -0.23 (0.20), residues: 600
  loop : -1.37 (0.19), residues: 1005

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 575 
 HIS   0.006   0.001   HIS A1195 
 PHE   0.023   0.002   PHE C 555 
 TYR   0.017   0.002   TYR D  43 
 ARG   0.012   0.001   ARG A 674 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05100 (  405)
  hydrogen bonds       : angle       6.49302 ( 1044)
  covalent geometry    : bond        0.00564 (14006)
  covalent geometry    : angle       0.63990 (19019)

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

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

  3446 Ramachandran restraints generated.
    1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3446 Ramachandran restraints generated.
    1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 135
  time to evaluate  : 1.676 
Fit side-chains
TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  106 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7786 (tt0)
REVERT: A  646 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.8219 (t80)
REVERT: A  656 TYR cc_start: 0.7586 (m-10) cc_final: 0.7351 (m-10)
REVERT: A  688 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7422 (mtp-110)
REVERT: A  727 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6341 (tm-30)
REVERT: A 1098 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7865 (ttp)
REVERT: A 1228 MET cc_start: 0.8704 (ptp) cc_final: 0.8492 (ptm)
REVERT: B   22 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.6925 (mt-10)
REVERT: D  383 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7071 (pp)
  outliers start: 86
  outliers final: 43
  residues processed: 198
  average time/residue: 0.8805
  time to fit residues: 198.9718
Evaluate side-chains
  179 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 129
  time to evaluate  : 1.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  552 VAL
Chi-restraints excluded: chain A residue   62 ASP
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue  106 GLU
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  403 SER
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  526 VAL
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain A residue  608 HIS
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  636 THR
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  688 ARG
Chi-restraints excluded: chain A residue  727 GLU
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  943 THR
Chi-restraints excluded: chain A residue  958 VAL
Chi-restraints excluded: chain A residue  976 VAL
Chi-restraints excluded: chain A residue  983 VAL
Chi-restraints excluded: chain A residue 1014 VAL
Chi-restraints excluded: chain A residue 1048 THR
Chi-restraints excluded: chain A residue 1063 VAL
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1098 MET
Chi-restraints excluded: chain A residue 1183 MET
Chi-restraints excluded: chain A residue 1185 PHE
Chi-restraints excluded: chain A residue 1189 ASP
Chi-restraints excluded: chain A residue 1203 GLU
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1241 VAL
Chi-restraints excluded: chain B residue   22 GLU
Chi-restraints excluded: chain B residue   38 ASN
Chi-restraints excluded: chain B residue   78 ASN
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   88 SER
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain D residue  130 LEU
Chi-restraints excluded: chain D residue  172 ILE
Chi-restraints excluded: chain D residue  253 CYS
Chi-restraints excluded: chain D residue  254 ILE
Chi-restraints excluded: chain D residue  262 HIS
Chi-restraints excluded: chain D residue  293 TYR
Chi-restraints excluded: chain D residue  383 ILE
Chi-restraints excluded: chain D residue  392 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 113 optimal weight:    0.5980
   chunk 33 optimal weight:    5.9990
   chunk 98 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 170 optimal weight:    5.9990
   chunk 85 optimal weight:    5.9990
   chunk 161 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 172 optimal weight:    1.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 146 HIS
A 232 GLN
** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 788 ASN
A1012 ASN
B  62 GLN
D 188 ASN
D 211 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.121007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.101769 restraints weight = 24110.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 2.10
r_work: 0.3312 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.1197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  14006  Z= 0.134
  Angle     :  0.548  11.256  19019  Z= 0.288
  Chirality :  0.047   0.148   2182
  Planarity :  0.004   0.043   2426
  Dihedral  :  6.279  59.308   1904
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 22.91 %
    Favored  : 72.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.19), residues: 1723
  helix: -0.70 (0.49), residues: 113
  sheet: -0.23 (0.20), residues: 593
  loop : -1.29 (0.19), residues: 1017

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 312 
 HIS   0.004   0.001   HIS A1195 
 PHE   0.014   0.001   PHE A1218 
 TYR   0.016   0.001   TYR D  43 
 ARG   0.004   0.000   ARG A 612 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04017 (  405)
  hydrogen bonds       : angle       6.16803 ( 1044)
  covalent geometry    : bond        0.00302 (14006)
  covalent geometry    : angle       0.54828 (19019)

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

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

  3446 Ramachandran restraints generated.
    1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3446 Ramachandran restraints generated.
    1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 143
  time to evaluate  : 1.615 
Fit side-chains
TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  598 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7754 (tp)
REVERT: A  656 TYR cc_start: 0.7515 (m-10) cc_final: 0.6664 (m-10)
REVERT: A  727 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6276 (tm-30)
REVERT: B   22 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.6809 (mt-10)
REVERT: D  211 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7291 (tp-100)
REVERT: D  383 ILE cc_start: 0.7404 (OUTLIER) cc_final: 0.6983 (pp)
  outliers start: 74
  outliers final: 36
  residues processed: 196
  average time/residue: 0.8868
  time to fit residues: 198.4361
Evaluate side-chains
  172 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 131
  time to evaluate  : 1.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  552 VAL
Chi-restraints excluded: chain A residue   62 ASP
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  403 SER
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  526 VAL
Chi-restraints excluded: chain A residue  598 ILE
Chi-restraints excluded: chain A residue  608 HIS
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  727 GLU
Chi-restraints excluded: chain A residue  943 THR
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue  958 VAL
Chi-restraints excluded: chain A residue  977 ILE
Chi-restraints excluded: chain A residue  983 VAL
Chi-restraints excluded: chain A residue 1014 VAL
Chi-restraints excluded: chain A residue 1048 THR
Chi-restraints excluded: chain A residue 1089 THR
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1183 MET
Chi-restraints excluded: chain A residue 1185 PHE
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1241 VAL
Chi-restraints excluded: chain B residue   22 GLU
Chi-restraints excluded: chain B residue   78 ASN
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain D residue  130 LEU
Chi-restraints excluded: chain D residue  172 ILE
Chi-restraints excluded: chain D residue  187 SER
Chi-restraints excluded: chain D residue  211 GLN
Chi-restraints excluded: chain D residue  254 ILE
Chi-restraints excluded: chain D residue  293 TYR
Chi-restraints excluded: chain D residue  383 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 148 optimal weight:    4.9990
   chunk 144 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   chunk 111 optimal weight:    5.9990
   chunk 68 optimal weight:    6.9990
   chunk 147 optimal weight:    1.9990
   chunk 155 optimal weight:    2.9990
   chunk 142 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 153 optimal weight:    7.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 212 ASN
A 660 HIS
A 729 GLN
** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1012 ASN
** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  62 GLN
D 188 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.116873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.097502 restraints weight = 24354.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 2.08
r_work: 0.3242 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3131 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.1457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061  14006  Z= 0.319
  Angle     :  0.694  15.341  19019  Z= 0.364
  Chirality :  0.051   0.179   2182
  Planarity :  0.005   0.042   2426
  Dihedral  :  6.818  50.806   1899
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 22.25 %
    Favored  : 71.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.19), residues: 1723
  helix: -0.84 (0.48), residues: 112
  sheet: -0.27 (0.20), residues: 603
  loop : -1.49 (0.19), residues: 1008

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 575 
 HIS   0.010   0.001   HIS A1195 
 PHE   0.016   0.002   PHE A1218 
 TYR   0.020   0.002   TYR A 250 
 ARG   0.005   0.001   ARG A 674 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05159 (  405)
  hydrogen bonds       : angle       6.48127 ( 1044)
  covalent geometry    : bond        0.00731 (14006)
  covalent geometry    : angle       0.69446 (19019)

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

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

  3446 Ramachandran restraints generated.
    1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3446 Ramachandran restraints generated.
    1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 91
    poor density    : 137
  time to evaluate  : 1.519 
Fit side-chains
TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  106 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7751 (tt0)
REVERT: A  125 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8170 (mmm)
REVERT: A  598 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7756 (tp)
REVERT: A  688 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7459 (mtp-110)
REVERT: A  727 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6347 (tm-30)
REVERT: A 1098 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7889 (ttp)
REVERT: D  104 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7855 (pp20)
REVERT: D  169 VAL cc_start: 0.8664 (t) cc_final: 0.8445 (p)
REVERT: D  383 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7122 (pp)
  outliers start: 91
  outliers final: 57
  residues processed: 204
  average time/residue: 0.8264
  time to fit residues: 192.3457
Evaluate side-chains
  195 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 130
  time to evaluate  : 1.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  552 VAL
Chi-restraints excluded: chain A residue   62 ASP
Chi-restraints excluded: chain A residue   75 CYS
Chi-restraints excluded: chain A residue  106 GLU
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  125 MET
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  268 SER
Chi-restraints excluded: chain A residue  269 THR
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain A residue  403 SER
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  526 VAL
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  598 ILE
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain A residue  608 HIS
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  636 THR
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain A residue  655 ASP
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  688 ARG
Chi-restraints excluded: chain A residue  700 ASN
Chi-restraints excluded: chain A residue  727 GLU
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  943 THR
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue  958 VAL
Chi-restraints excluded: chain A residue  974 GLU
Chi-restraints excluded: chain A residue  976 VAL
Chi-restraints excluded: chain A residue  977 ILE
Chi-restraints excluded: chain A residue  983 VAL
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1004 ILE
Chi-restraints excluded: chain A residue 1014 VAL
Chi-restraints excluded: chain A residue 1048 THR
Chi-restraints excluded: chain A residue 1060 ILE
Chi-restraints excluded: chain A residue 1089 THR
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1098 MET
Chi-restraints excluded: chain A residue 1123 ASP
Chi-restraints excluded: chain A residue 1183 MET
Chi-restraints excluded: chain A residue 1185 PHE
Chi-restraints excluded: chain A residue 1203 GLU
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1241 VAL
Chi-restraints excluded: chain B residue   38 ASN
Chi-restraints excluded: chain B residue   78 ASN
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue  104 GLU
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain D residue  130 LEU
Chi-restraints excluded: chain D residue  172 ILE
Chi-restraints excluded: chain D residue  187 SER
Chi-restraints excluded: chain D residue  253 CYS
Chi-restraints excluded: chain D residue  254 ILE
Chi-restraints excluded: chain D residue  293 TYR
Chi-restraints excluded: chain D residue  383 ILE
Chi-restraints excluded: chain D residue  392 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 59 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 149 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   chunk 142 optimal weight:    2.9990
   chunk 168 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9990
   chunk 82 optimal weight:    0.7980
   chunk 134 optimal weight:    3.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 146 HIS
A 417 ASN
** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1012 ASN
B  62 GLN
D 188 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.120840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.101666 restraints weight = 24424.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 2.10
r_work: 0.3312 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.1357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14006  Z= 0.128
  Angle     :  0.557  11.248  19019  Z= 0.290
  Chirality :  0.047   0.146   2182
  Planarity :  0.004   0.041   2426
  Dihedral  :  6.285  58.388   1899
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 23.84 %
    Favored  : 71.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.19), residues: 1723
  helix: -0.69 (0.49), residues: 113
  sheet: -0.24 (0.20), residues: 588
  loop : -1.36 (0.19), residues: 1022

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 312 
 HIS   0.003   0.001   HIS A1195 
 PHE   0.015   0.001   PHE D 332 
 TYR   0.016   0.001   TYR A1157 
 ARG   0.003   0.000   ARG A 612 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03788 (  405)
  hydrogen bonds       : angle       6.08492 ( 1044)
  covalent geometry    : bond        0.00289 (14006)
  covalent geometry    : angle       0.55690 (19019)

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

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

  3446 Ramachandran restraints generated.
    1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3446 Ramachandran restraints generated.
    1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 143
  time to evaluate  : 1.630 
Fit side-chains
TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  106 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7675 (tt0)
REVERT: A  336 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7923 (mtt)
REVERT: A  598 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7727 (tp)
REVERT: A  727 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6008 (tm-30)
REVERT: D  131 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7939 (ttm)
REVERT: D  136 SER cc_start: 0.8713 (OUTLIER) cc_final: 0.8175 (p)
REVERT: D  220 TRP cc_start: 0.7316 (OUTLIER) cc_final: 0.6051 (t-100)
REVERT: D  221 ASP cc_start: 0.7101 (t70) cc_final: 0.6829 (t70)
REVERT: D  383 ILE cc_start: 0.7385 (OUTLIER) cc_final: 0.6954 (pp)
  outliers start: 71
  outliers final: 41
  residues processed: 192
  average time/residue: 0.9172
  time to fit residues: 201.0206
Evaluate side-chains
  180 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 131
  time to evaluate  : 1.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  552 VAL
Chi-restraints excluded: chain A residue   62 ASP
Chi-restraints excluded: chain A residue  106 GLU
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  268 SER
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain A residue  403 SER
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  526 VAL
Chi-restraints excluded: chain A residue  598 ILE
Chi-restraints excluded: chain A residue  608 HIS
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain A residue  655 ASP
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  727 GLU
Chi-restraints excluded: chain A residue  943 THR
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue  958 VAL
Chi-restraints excluded: chain A residue  977 ILE
Chi-restraints excluded: chain A residue  983 VAL
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1014 VAL
Chi-restraints excluded: chain A residue 1048 THR
Chi-restraints excluded: chain A residue 1089 THR
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1183 MET
Chi-restraints excluded: chain A residue 1185 PHE
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1241 VAL
Chi-restraints excluded: chain B residue   78 ASN
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain D residue  131 MET
Chi-restraints excluded: chain D residue  136 SER
Chi-restraints excluded: chain D residue  172 ILE
Chi-restraints excluded: chain D residue  200 ILE
Chi-restraints excluded: chain D residue  220 TRP
Chi-restraints excluded: chain D residue  253 CYS
Chi-restraints excluded: chain D residue  254 ILE
Chi-restraints excluded: chain D residue  293 TYR
Chi-restraints excluded: chain D residue  295 MET
Chi-restraints excluded: chain D residue  383 ILE
Chi-restraints excluded: chain D residue  392 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 155 optimal weight:    5.9990
   chunk 31 optimal weight:    9.9990
   chunk 91 optimal weight:    2.9990
   chunk 88 optimal weight:    0.8980
   chunk 166 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 79 optimal weight:    4.9990
   chunk 115 optimal weight:    0.3980
   chunk 64 optimal weight:    5.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 376 GLN
** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1012 ASN
B  62 GLN
D 188 ASN
D 211 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.121114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.101998 restraints weight = 24201.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 2.08
r_work: 0.3316 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.1389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  14006  Z= 0.132
  Angle     :  0.553  10.733  19019  Z= 0.288
  Chirality :  0.047   0.144   2182
  Planarity :  0.004   0.041   2426
  Dihedral  :  6.100  50.934   1898
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 24.57 %
    Favored  : 70.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.19), residues: 1723
  helix: -0.52 (0.50), residues: 113
  sheet: -0.23 (0.20), residues: 584
  loop : -1.33 (0.19), residues: 1026

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 312 
 HIS   0.004   0.001   HIS A 282 
 PHE   0.014   0.001   PHE D 320 
 TYR   0.017   0.001   TYR B  23 
 ARG   0.007   0.000   ARG A 674 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03772 (  405)
  hydrogen bonds       : angle       5.95878 ( 1044)
  covalent geometry    : bond        0.00300 (14006)
  covalent geometry    : angle       0.55263 (19019)

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

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

  3446 Ramachandran restraints generated.
    1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3446 Ramachandran restraints generated.
    1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 135
  time to evaluate  : 1.555 
Fit side-chains
TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  336 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7932 (mtt)
REVERT: A  598 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7731 (tp)
REVERT: A  727 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6014 (tm-30)
REVERT: A  909 LYS cc_start: 0.8058 (mmtt) cc_final: 0.7835 (mmpt)
REVERT: B   22 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.6867 (mt-10)
REVERT: D  131 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7929 (ttm)
REVERT: D  136 SER cc_start: 0.8699 (OUTLIER) cc_final: 0.8159 (p)
REVERT: D  221 ASP cc_start: 0.7106 (t70) cc_final: 0.6865 (t70)
REVERT: D  383 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.6954 (pp)
  outliers start: 68
  outliers final: 42
  residues processed: 186
  average time/residue: 1.0172
  time to fit residues: 217.3152
Evaluate side-chains
  177 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 128
  time to evaluate  : 3.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  552 VAL
Chi-restraints excluded: chain A residue   62 ASP
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  268 SER
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain A residue  403 SER
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  526 VAL
Chi-restraints excluded: chain A residue  598 ILE
Chi-restraints excluded: chain A residue  608 HIS
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain A residue  655 ASP
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  727 GLU
Chi-restraints excluded: chain A residue  943 THR
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue  976 VAL
Chi-restraints excluded: chain A residue  977 ILE
Chi-restraints excluded: chain A residue  983 VAL
Chi-restraints excluded: chain A residue 1004 ILE
Chi-restraints excluded: chain A residue 1014 VAL
Chi-restraints excluded: chain A residue 1048 THR
Chi-restraints excluded: chain A residue 1089 THR
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1183 MET
Chi-restraints excluded: chain A residue 1185 PHE
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1241 VAL
Chi-restraints excluded: chain B residue   22 GLU
Chi-restraints excluded: chain B residue   78 ASN
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   88 SER
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain D residue  130 LEU
Chi-restraints excluded: chain D residue  131 MET
Chi-restraints excluded: chain D residue  136 SER
Chi-restraints excluded: chain D residue  172 ILE
Chi-restraints excluded: chain D residue  254 ILE
Chi-restraints excluded: chain D residue  293 TYR
Chi-restraints excluded: chain D residue  295 MET
Chi-restraints excluded: chain D residue  383 ILE
Chi-restraints excluded: chain D residue  392 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 149 optimal weight:    6.9990
   chunk 93 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 90 optimal weight:    7.9990
   chunk 169 optimal weight:    5.9990
   chunk 21 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 30 optimal weight:    7.9990
   chunk 8 optimal weight:    5.9990
   chunk 110 optimal weight:    2.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 660 HIS
** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1012 ASN
B  62 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.119325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.100085 restraints weight = 24271.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 2.09
r_work: 0.3285 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.1425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14006  Z= 0.196
  Angle     :  0.599  12.459  19019  Z= 0.312
  Chirality :  0.048   0.145   2182
  Planarity :  0.004   0.073   2426
  Dihedral  :  6.321  50.481   1898
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 24.11 %
    Favored  : 70.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.20), residues: 1723
  helix: -0.64 (0.49), residues: 113
  sheet: -0.26 (0.20), residues: 600
  loop : -1.34 (0.19), residues: 1010

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 575 
 HIS   0.005   0.001   HIS A1195 
 PHE   0.014   0.002   PHE A1218 
 TYR   0.021   0.002   TYR B  23 
 ARG   0.003   0.000   ARG A 674 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04206 (  405)
  hydrogen bonds       : angle       6.09485 ( 1044)
  covalent geometry    : bond        0.00448 (14006)
  covalent geometry    : angle       0.59915 (19019)

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

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

  3446 Ramachandran restraints generated.
    1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3446 Ramachandran restraints generated.
    1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 136
  time to evaluate  : 1.884 
Fit side-chains
TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  598 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7716 (tp)
REVERT: A  727 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6090 (tm-30)
REVERT: D  131 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7922 (ttm)
REVERT: D  221 ASP cc_start: 0.7119 (t70) cc_final: 0.6896 (t70)
REVERT: D  383 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7066 (pp)
  outliers start: 74
  outliers final: 50
  residues processed: 190
  average time/residue: 1.1376
  time to fit residues: 246.8003
Evaluate side-chains
  187 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 133
  time to evaluate  : 1.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  552 VAL
Chi-restraints excluded: chain A residue   62 ASP
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  268 SER
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  403 SER
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  526 VAL
Chi-restraints excluded: chain A residue  598 ILE
Chi-restraints excluded: chain A residue  608 HIS
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  636 THR
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain A residue  655 ASP
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  727 GLU
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  943 THR
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue  958 VAL
Chi-restraints excluded: chain A residue  976 VAL
Chi-restraints excluded: chain A residue  977 ILE
Chi-restraints excluded: chain A residue  983 VAL
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1014 VAL
Chi-restraints excluded: chain A residue 1048 THR
Chi-restraints excluded: chain A residue 1089 THR
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1183 MET
Chi-restraints excluded: chain A residue 1185 PHE
Chi-restraints excluded: chain A residue 1203 GLU
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1241 VAL
Chi-restraints excluded: chain B residue   30 ASP
Chi-restraints excluded: chain B residue   38 ASN
Chi-restraints excluded: chain B residue   78 ASN
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   88 SER
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain D residue  130 LEU
Chi-restraints excluded: chain D residue  131 MET
Chi-restraints excluded: chain D residue  136 SER
Chi-restraints excluded: chain D residue  172 ILE
Chi-restraints excluded: chain D residue  253 CYS
Chi-restraints excluded: chain D residue  254 ILE
Chi-restraints excluded: chain D residue  293 TYR
Chi-restraints excluded: chain D residue  383 ILE
Chi-restraints excluded: chain D residue  392 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 102 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 159 optimal weight:    0.6980
   chunk 114 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 72 optimal weight:    3.9990
   chunk 156 optimal weight:    0.9990
   chunk 127 optimal weight:    0.0970
   chunk 61 optimal weight:    0.7980
   chunk 163 optimal weight:    5.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1012 ASN
B  62 GLN
D 188 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.122146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.103107 restraints weight = 24198.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.10
r_work: 0.3335 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.1465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14006  Z= 0.114
  Angle     :  0.544   9.657  19019  Z= 0.283
  Chirality :  0.046   0.146   2182
  Planarity :  0.004   0.049   2426
  Dihedral  :  5.945  50.361   1898
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 24.90 %
    Favored  : 71.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.20), residues: 1723
  helix: -0.50 (0.51), residues: 113
  sheet: -0.22 (0.20), residues: 578
  loop : -1.29 (0.19), residues: 1032

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 312 
 HIS   0.004   0.001   HIS A 282 
 PHE   0.014   0.001   PHE D 332 
 TYR   0.023   0.001   TYR B  23 
 ARG   0.006   0.000   ARG A 674 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03516 (  405)
  hydrogen bonds       : angle       5.90030 ( 1044)
  covalent geometry    : bond        0.00259 (14006)
  covalent geometry    : angle       0.54390 (19019)

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

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

  3446 Ramachandran restraints generated.
    1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3446 Ramachandran restraints generated.
    1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 135
  time to evaluate  : 1.485 
Fit side-chains
TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  198 SER cc_start: 0.7578 (m) cc_final: 0.7377 (p)
REVERT: A  598 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7740 (tp)
REVERT: A  727 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6064 (tm-30)
REVERT: B   22 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6825 (mt-10)
REVERT: D  131 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7897 (ttm)
REVERT: D  136 SER cc_start: 0.8706 (OUTLIER) cc_final: 0.8161 (p)
REVERT: D  220 TRP cc_start: 0.7300 (OUTLIER) cc_final: 0.6036 (t-100)
REVERT: D  221 ASP cc_start: 0.7081 (t70) cc_final: 0.6804 (t70)
REVERT: D  383 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.6935 (pp)
  outliers start: 61
  outliers final: 42
  residues processed: 183
  average time/residue: 0.8435
  time to fit residues: 177.6555
Evaluate side-chains
  176 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 127
  time to evaluate  : 1.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  552 VAL
Chi-restraints excluded: chain A residue   62 ASP
Chi-restraints excluded: chain A residue  121 SER
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  268 SER
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  403 SER
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  526 VAL
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  598 ILE
Chi-restraints excluded: chain A residue  608 HIS
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  636 THR
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain A residue  655 ASP
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  700 ASN
Chi-restraints excluded: chain A residue  727 GLU
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  943 THR
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue  958 VAL
Chi-restraints excluded: chain A residue  976 VAL
Chi-restraints excluded: chain A residue  977 ILE
Chi-restraints excluded: chain A residue  983 VAL
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1048 THR
Chi-restraints excluded: chain A residue 1089 THR
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1183 MET
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1241 VAL
Chi-restraints excluded: chain B residue   22 GLU
Chi-restraints excluded: chain B residue   78 ASN
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   88 SER
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain D residue  131 MET
Chi-restraints excluded: chain D residue  136 SER
Chi-restraints excluded: chain D residue  172 ILE
Chi-restraints excluded: chain D residue  220 TRP
Chi-restraints excluded: chain D residue  254 ILE
Chi-restraints excluded: chain D residue  293 TYR
Chi-restraints excluded: chain D residue  383 ILE
Chi-restraints excluded: chain D residue  392 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 134 optimal weight:    0.9990
   chunk 101 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 160 optimal weight:    8.9990
   chunk 118 optimal weight:    0.8980
   chunk 103 optimal weight:    0.6980
   chunk 83 optimal weight:    5.9990
   chunk 143 optimal weight:    6.9990
   chunk 68 optimal weight:    0.6980
   chunk 84 optimal weight:    3.9990
   chunk 107 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1012 ASN
B  62 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.122422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.103396 restraints weight = 24042.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.08
r_work: 0.3339 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14006  Z= 0.119
  Angle     :  0.551   9.870  19019  Z= 0.286
  Chirality :  0.047   0.146   2182
  Planarity :  0.004   0.046   2426
  Dihedral  :  5.792  50.185   1893
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 25.30 %
    Favored  : 70.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.20), residues: 1723
  helix: -0.46 (0.51), residues: 113
  sheet: -0.22 (0.20), residues: 584
  loop : -1.28 (0.19), residues: 1026

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 312 
 HIS   0.003   0.001   HIS A 282 
 PHE   0.015   0.001   PHE C 555 
 TYR   0.026   0.001   TYR B  23 
 ARG   0.005   0.000   ARG A 674 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03575 (  405)
  hydrogen bonds       : angle       5.85413 ( 1044)
  covalent geometry    : bond        0.00273 (14006)
  covalent geometry    : angle       0.55145 (19019)

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

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

  3446 Ramachandran restraints generated.
    1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3446 Ramachandran restraints generated.
    1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 137
  time to evaluate  : 1.477 
Fit side-chains
TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A  598 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7734 (tp)
REVERT: A  727 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6059 (tm-30)
REVERT: A 1159 MET cc_start: 0.8656 (mmm) cc_final: 0.8429 (mtp)
REVERT: D  131 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7896 (ttm)
REVERT: D  136 SER cc_start: 0.8693 (OUTLIER) cc_final: 0.8158 (p)
REVERT: D  221 ASP cc_start: 0.7070 (t70) cc_final: 0.6859 (t70)
REVERT: D  383 ILE cc_start: 0.7369 (OUTLIER) cc_final: 0.6934 (pp)
  outliers start: 57
  outliers final: 41
  residues processed: 182
  average time/residue: 1.0664
  time to fit residues: 223.9475
Evaluate side-chains
  175 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 129
  time to evaluate  : 1.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  552 VAL
Chi-restraints excluded: chain A residue   62 ASP
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  403 SER
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  515 THR
Chi-restraints excluded: chain A residue  526 VAL
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  598 ILE
Chi-restraints excluded: chain A residue  608 HIS
Chi-restraints excluded: chain A residue  613 LEU
Chi-restraints excluded: chain A residue  636 THR
Chi-restraints excluded: chain A residue  644 THR
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain A residue  655 ASP
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  668 ILE
Chi-restraints excluded: chain A residue  700 ASN
Chi-restraints excluded: chain A residue  727 GLU
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  943 THR
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue  958 VAL
Chi-restraints excluded: chain A residue  977 ILE
Chi-restraints excluded: chain A residue  983 VAL
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1048 THR
Chi-restraints excluded: chain A residue 1089 THR
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1183 MET
Chi-restraints excluded: chain A residue 1213 VAL
Chi-restraints excluded: chain A residue 1241 VAL
Chi-restraints excluded: chain B residue   78 ASN
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   88 SER
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain D residue  131 MET
Chi-restraints excluded: chain D residue  136 SER
Chi-restraints excluded: chain D residue  172 ILE
Chi-restraints excluded: chain D residue  187 SER
Chi-restraints excluded: chain D residue  254 ILE
Chi-restraints excluded: chain D residue  293 TYR
Chi-restraints excluded: chain D residue  383 ILE
Chi-restraints excluded: chain D residue  392 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 164 optimal weight:    7.9990
   chunk 129 optimal weight:   30.0000
   chunk 165 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0070
   chunk 10 optimal weight:    5.9990
   chunk 48 optimal weight:    0.7980
   chunk 112 optimal weight:    2.9990
   chunk 171 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 123 optimal weight:    9.9990
   chunk 130 optimal weight:    9.9990
   overall best weight:    1.1002

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

Flipped N/Q/H residues before XYZ refinement:
** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1012 ASN
B  62 GLN
D 188 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.121765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.102620 restraints weight = 24360.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 2.11
r_work: 0.3326 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14006  Z= 0.138
  Angle     :  0.566  10.706  19019  Z= 0.292
  Chirality :  0.047   0.146   2182
  Planarity :  0.004   0.046   2426
  Dihedral  :  5.799  49.876   1893
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 25.50 %
    Favored  : 71.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.20), residues: 1723
  helix: -0.51 (0.50), residues: 113
  sheet: -0.20 (0.20), residues: 584
  loop : -1.28 (0.19), residues: 1026

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 312 
 HIS   0.003   0.001   HIS A 282 
 PHE   0.014   0.001   PHE A1185 
 TYR   0.024   0.001   TYR B  23 
 ARG   0.005   0.000   ARG A 674 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03681 (  405)
  hydrogen bonds       : angle       5.87195 ( 1044)
  covalent geometry    : bond        0.00318 (14006)
  covalent geometry    : angle       0.56571 (19019)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9531.06 seconds
wall clock time: 170 minutes 28.74 seconds (10228.74 seconds total)