Starting phenix.real_space_refine
on Sat Aug 23 14:28:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e3q_27870/08_2025/8e3q_27870.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e3q_27870/08_2025/8e3q_27870.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8e3q_27870/08_2025/8e3q_27870.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e3q_27870/08_2025/8e3q_27870.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e3q_27870/08_2025/8e3q_27870.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e3q_27870/08_2025/8e3q_27870.cif"
  }
  resolution = 2.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.124
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      80      5.16       5
     C    8157      2.51       5
     N    2214      2.21       5
     O    2287      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12739
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1178, 9348
          Classifications: {'peptide': 1178}
          Link IDs: {'PTRANS': 66, 'TRANS': 1111}
          Chain breaks: 13
    Chain: "C"
      Number of atoms: 448
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 448
          Classifications: {'peptide': 60}
          Link IDs: {'PTRANS': 4, 'TRANS': 55}
    Chain: "B"
      Number of atoms: 2942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 365, 2942
          Classifications: {'peptide': 365}
          Link IDs: {'PTRANS': 15, 'TRANS': 349}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   9658  SG  CYS C  41      29.296  90.239  96.332  1.00 72.45           S
  ATOM   9722  SG  CYS C  49      26.663  91.779  98.639  1.00 80.81           S
  ATOM   9757  SG  CYS C  55      27.485  88.030  98.906  1.00 77.72           S

  Time building chain proxies: 3.25, per 1000 atoms: 0.26
  Number of scatterers: 12739
  At special positions: 0
  Unit cell: (87.98, 107.07, 134.46, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      80     16.00
     O    2287      8.00
     N    2214      7.00
     C    8157      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: 1.69
  Conformation dependent library (CDL) restraints added in 617.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN C 301 "
        pdb="ZN    ZN C 301 " - pdb=" NE2 HIS C  59 "
        pdb="ZN    ZN C 301 " - pdb=" SG  CYS C  49 "
        pdb="ZN    ZN C 301 " - pdb=" SG  CYS C  41 "
        pdb="ZN    ZN C 301 " - pdb=" SG  CYS C  55 "
      Number of angles added : 3


  3142 Ramachandran restraints generated.
    1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2998

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 30 sheets defined
      9.3% alpha, 37.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 125 through 130
      removed outlier: 3.584A  pdb=" N   ARG A 129 " --> pdb=" O   GLU A 125 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ASP A 130 " --> pdb=" O   PRO A 126 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 125 through 130'
    Processing helix  chain 'A' and resid 194 through 196
      No H-bonds generated for 'chain 'A' and resid 194 through 196'
    Processing helix  chain 'A' and resid 230 through 234
    Processing helix  chain 'A' and resid 301 through 305
      removed outlier: 3.588A  pdb=" N   THR A 304 " --> pdb=" O   ASN A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 509
    Processing helix  chain 'A' and resid 1153 through 1156
    Processing helix  chain 'A' and resid 1352 through 1370
    Processing helix  chain 'A' and resid 1372 through 1376
    Processing helix  chain 'A' and resid 1377 through 1383
    Processing helix  chain 'A' and resid 1401 through 1410
      removed outlier: 4.152A  pdb=" N   ARG A1406 " --> pdb=" O   GLU A1402 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   TYR A1407 " --> pdb=" O   LEU A1403 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   LEU A1408 " --> pdb=" O   LEU A1404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1411 through 1422
    Processing helix  chain 'A' and resid 1425 through 1440
      removed outlier: 3.719A  pdb=" N   THR A1440 " --> pdb=" O   THR A1436 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1 through 6
      removed outlier: 3.819A  pdb=" N   ILE C   5 " --> pdb=" O   MET C   1 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 13 through 22
    Processing helix  chain 'C' and resid 41 through 46
      removed outlier: 3.530A  pdb=" N   LEU C  45 " --> pdb=" O   CYS C  41 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LYS C  46 " --> pdb=" O   GLU C  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 41 through 46'
    Processing helix  chain 'B' and resid 59 through 73
      removed outlier: 3.546A  pdb=" N   ILE B  71 " --> pdb=" O   LEU B  67 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   TRP B  72 " --> pdb=" O   GLU B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 79
    Processing helix  chain 'B' and resid 88 through 92
      removed outlier: 3.749A  pdb=" N   ASP B  91 " --> pdb=" O   TYR B  88 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU B  92 " --> pdb=" O   TYR B  89 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 88 through 92'
    Processing helix  chain 'B' and resid 101 through 106
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1308 through 1315
      removed outlier: 4.157A  pdb=" N   THR A1310 " --> pdb=" O   ALA A1339 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ALA A1339 " --> pdb=" O   THR A1310 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   HIS A1334 " --> pdb=" O   PRO A1350 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   LEU A1347 " --> pdb=" O   GLN A   7 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   GLN A   7 " --> pdb=" O   LEU A1347 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   LEU A1349 " --> pdb=" O   TYR A   5 " (cutoff:3.500A)
      removed outlier: 5.615A  pdb=" N   TYR A   5 " --> pdb=" O   LEU A1349 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 24
      removed outlier: 4.674A  pdb=" N   PHE A  22 " --> pdb=" O   GLU A  27 " (cutoff:3.500A)
      removed outlier: 9.030A  pdb=" N   GLU A  27 " --> pdb=" O   PHE A  22 " (cutoff:3.500A)
      removed outlier: 9.381A  pdb=" N   ARG A  28 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   LEU A  43 " --> pdb=" O   ARG A  28 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   LEU A  38 " --> pdb=" O   SER A  71 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   SER A  71 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   VAL A  40 " --> pdb=" O   ALA A  69 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 84
      removed outlier: 3.566A  pdb=" N   SER A  80 " --> pdb=" O   SER A  97 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LYS A 102 " --> pdb=" O   PHE A  98 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   LEU A 103 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   LEU A 120 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   VAL A 105 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 143
    Processing sheet with id=AA5, first strand: chain 'A' and resid 205 through 208
      removed outlier: 6.493A  pdb=" N   CYS A 238 " --> pdb=" O   SER A 260 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   SER A 260 " --> pdb=" O   CYS A 238 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   TRP A 256 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   SER A 244 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   VAL A 254 " --> pdb=" O   SER A 244 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 270
      removed outlier: 3.673A  pdb=" N   SER A 285 " --> pdb=" O   ALA A 282 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 331
      removed outlier: 3.865A  pdb=" N   ILE A 330 " --> pdb=" O   LYS A 334 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   LYS A 334 " --> pdb=" O   ILE A 330 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 373 through 376
      removed outlier: 6.316A  pdb=" N   SER A 391 " --> pdb=" O   SER A 468 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   SER A 468 " --> pdb=" O   SER A 391 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   LEU A 393 " --> pdb=" O   CYS A 466 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 477 through 481
      removed outlier: 4.103A  pdb=" N   ASN A 477 " --> pdb=" O   CYS A 503 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 522 through 528
      removed outlier: 6.742A  pdb=" N   ILE A 998 " --> pdb=" O   VAL A 524 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   THR A 526 " --> pdb=" O   LEU A 996 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   LEU A 996 " --> pdb=" O   THR A 526 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   GLU A 995 " --> pdb=" O   ASN A 991 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   TYR A 989 " --> pdb=" O   ARG A 997 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   SER A 974 " --> pdb=" O   PHE A 990 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 534 through 539
      removed outlier: 3.895A  pdb=" N   ASP A 534 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   PHE A 574 " --> pdb=" O   VAL A 538 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 608 through 612
      removed outlier: 3.602A  pdb=" N   TYR A 617 " --> pdb=" O   ILE A 612 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   ILE A 626 " --> pdb=" O   PHE A 637 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   PHE A 637 " --> pdb=" O   ILE A 626 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   LEU A 628 " --> pdb=" O   LEU A 635 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 646 through 651
    Processing sheet with id=AB5, first strand: chain 'A' and resid 695 through 703
      removed outlier: 3.649A  pdb=" N   THR A 697 " --> pdb=" O   VAL A 788 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   MET A 794 " --> pdb=" O   LEU A 807 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   LEU A 807 " --> pdb=" O   MET A 794 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   ILE A 796 " --> pdb=" O   VAL A 805 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG A 803 " --> pdb=" O   GLN A 798 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 817 through 818
      removed outlier: 3.505A  pdb=" N   PHE A 892 " --> pdb=" O   LEU A 818 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 931 through 937
      removed outlier: 5.550A  pdb=" N   TYR A 940 " --> pdb=" O   ASP A 936 " (cutoff:3.500A)
      removed outlier: 5.078A  pdb=" N   SER A 941 " --> pdb=" O   VAL A 955 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   VAL A 955 " --> pdb=" O   SER A 941 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1021 through 1027
      removed outlier: 5.441A  pdb=" N   ALA A1022 " --> pdb=" O   SER A1039 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   SER A1039 " --> pdb=" O   ALA A1022 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   TYR A1024 " --> pdb=" O   ALA A1037 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 1046 through 1049
    Processing sheet with id=AC1, first strand: chain 'A' and resid 1098 through 1106
      removed outlier: 5.468A  pdb=" N   VAL A1100 " --> pdb=" O   CYS A1126 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   CYS A1126 " --> pdb=" O   VAL A1100 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   ILE A1139 " --> pdb=" O   GLU A1165 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   GLU A1165 " --> pdb=" O   ILE A1139 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ILE A1141 " --> pdb=" O   LEU A1163 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 1172 through 1178
      removed outlier: 3.680A  pdb=" N   ALA A1174 " --> pdb=" O   ALA A1185 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   ILE A1190 " --> pdb=" O   PHE A1205 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   PHE A1205 " --> pdb=" O   ILE A1190 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   LEU A1192 " --> pdb=" O   MET A1203 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ARG A1196 " --> pdb=" O   GLU A1199 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'A' and resid 1212 through 1218
      removed outlier: 3.918A  pdb=" N   GLN A1214 " --> pdb=" O   ALA A1225 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   ARG A1235 " --> pdb=" O   LEU A1245 " (cutoff:3.500A)
      removed outlier: 5.475A  pdb=" N   LEU A1245 " --> pdb=" O   ARG A1235 " (cutoff:3.500A)
      removed outlier: 7.431A  pdb=" N   GLN A1237 " --> pdb=" O   LEU A1243 " (cutoff:3.500A)
      removed outlier: 5.982A  pdb=" N   LEU A1243 " --> pdb=" O   GLN A1237 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'A' and resid 1255 through 1258
      removed outlier: 6.795A  pdb=" N   SER A1272 " --> pdb=" O   TYR A1256 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   VAL A1258 " --> pdb=" O   LEU A1270 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   LEU A1270 " --> pdb=" O   VAL A1258 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'A' and resid 1255 through 1258
      removed outlier: 6.795A  pdb=" N   SER A1272 " --> pdb=" O   TYR A1256 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   VAL A1258 " --> pdb=" O   LEU A1270 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   LEU A1270 " --> pdb=" O   VAL A1258 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   MET A1282 " --> pdb=" O   ARG A1298 " (cutoff:3.500A)
      removed outlier: 5.811A  pdb=" N   ARG A1298 " --> pdb=" O   MET A1282 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 109 through 114
      removed outlier: 5.347A  pdb=" N   PHE B 110 " --> pdb=" O   THR B 403 " (cutoff:3.500A)
      removed outlier: 5.774A  pdb=" N   THR B 403 " --> pdb=" O   PHE B 110 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ARG B 112 " --> pdb=" O   PHE B 401 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 122 through 127
      removed outlier: 3.501A  pdb=" N   THR B 144 " --> pdb=" O   THR B 136 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ALA B 138 " --> pdb=" O   GLU B 142 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   GLU B 142 " --> pdb=" O   ALA B 138 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   PHE B 143 " --> pdb=" O   ILE B 156 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   ILE B 156 " --> pdb=" O   PHE B 143 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   LEU B 145 " --> pdb=" O   GLU B 154 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 164 through 169
      removed outlier: 4.552A  pdb=" N   TYR B 184 " --> pdb=" O   ASP B 180 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   LYS B 196 " --> pdb=" O   TYR B 187 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 205 through 210
      removed outlier: 6.870A  pdb=" N   CYS B 220 " --> pdb=" O   ARG B 206 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   ALA B 208 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   ALA B 218 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 5.077A  pdb=" N   PHE B 210 " --> pdb=" O   LYS B 216 " (cutoff:3.500A)
      removed outlier: 7.255A  pdb=" N   LYS B 216 " --> pdb=" O   PHE B 210 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ARG B 238 " --> pdb=" O   ILE B 228 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   ASP B 230 " --> pdb=" O   GLU B 236 " (cutoff:3.500A)
      removed outlier: 6.099A  pdb=" N   GLU B 236 " --> pdb=" O   ASP B 230 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'B' and resid 247 through 252
    Processing sheet with id=AD2, first strand: chain 'B' and resid 291 through 296
      removed outlier: 6.315A  pdb=" N   ALA B 306 " --> pdb=" O   MET B 292 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   VAL B 294 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   LEU B 304 " --> pdb=" O   VAL B 294 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   LEU B 296 " --> pdb=" O   TRP B 302 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   TRP B 302 " --> pdb=" O   LEU B 296 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'B' and resid 334 through 339
      removed outlier: 3.741A  pdb=" N   ALA B 336 " --> pdb=" O   GLY B 350 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY B 368 " --> pdb=" O   PHE B 358 " (cutoff:3.500A)

    430 hydrogen bonds defined for protein.
    1116 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: 3.25

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4144
        1.34 -     1.46: 2905
        1.46 -     1.58: 5869
        1.58 -     1.69: 0
        1.69 -     1.81: 129
  Bond restraints: 13047
  Sorted by residual:
  bond pdb=" N   GLN B 189 "
       pdb=" CA  GLN B 189 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.21e-02 6.83e+03 7.93e+00
  bond pdb=" N   TRP B 188 "
       pdb=" CA  TRP B 188 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.033 1.25e-02 6.40e+03 7.07e+00
  bond pdb=" N   TYR B 187 "
       pdb=" CA  TYR B 187 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.031 1.21e-02 6.83e+03 6.76e+00
  bond pdb=" N   SER B 190 "
       pdb=" CA  SER B 190 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.23e-02 6.61e+03 4.91e+00
  bond pdb=" CB  PRO A 494 "
       pdb=" CG  PRO A 494 "
    ideal  model  delta    sigma   weight residual
    1.492  1.568 -0.076 5.00e-02 4.00e+02 2.30e+00
  ... (remaining 13042 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 17267
        1.57 -     3.14: 359
        3.14 -     4.71: 58
        4.71 -     6.28: 11
        6.28 -     7.84: 1
  Bond angle restraints: 17696
  Sorted by residual:
  angle pdb=" C   TYR A 332 "
        pdb=" N   ASP A 333 "
        pdb=" CA  ASP A 333 "
      ideal   model   delta    sigma   weight residual
     121.54  129.38   -7.84 1.91e+00 2.74e-01 1.69e+01
  angle pdb=" N   VAL A 647 "
        pdb=" CA  VAL A 647 "
        pdb=" C   VAL A 647 "
      ideal   model   delta    sigma   weight residual
     113.53  110.26    3.27 9.80e-01 1.04e+00 1.12e+01
  angle pdb=" N   ASN B 289 "
        pdb=" CA  ASN B 289 "
        pdb=" C   ASN B 289 "
      ideal   model   delta    sigma   weight residual
     107.20  112.76   -5.56 1.70e+00 3.46e-01 1.07e+01
  angle pdb=" CA  GLN B 189 "
        pdb=" C   GLN B 189 "
        pdb=" O   GLN B 189 "
      ideal   model   delta    sigma   weight residual
     121.72  118.15    3.57 1.18e+00 7.18e-01 9.16e+00
  angle pdb=" N   GLU A1417 "
        pdb=" CA  GLU A1417 "
        pdb=" CB  GLU A1417 "
      ideal   model   delta    sigma   weight residual
     110.12  114.49   -4.37 1.47e+00 4.63e-01 8.83e+00
  ... (remaining 17691 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.72: 7139
       17.72 -    35.43: 514
       35.43 -    53.15: 87
       53.15 -    70.87: 22
       70.87 -    88.58: 9
  Dihedral angle restraints: 7771
    sinusoidal: 3134
      harmonic: 4637
  Sorted by residual:
  dihedral pdb=" CA  ASP A 936 "
           pdb=" C   ASP A 936 "
           pdb=" N   ILE A 937 "
           pdb=" CA  ILE A 937 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.24   23.76     0      5.00e+00 4.00e-02 2.26e+01
  dihedral pdb=" CA  GLN A  85 "
           pdb=" C   GLN A  85 "
           pdb=" N   LEU A  86 "
           pdb=" CA  LEU A  86 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.14  -17.86     0      5.00e+00 4.00e-02 1.28e+01
  dihedral pdb=" CA  HIS B 171 "
           pdb=" C   HIS B 171 "
           pdb=" N   ASN B 172 "
           pdb=" CA  ASN B 172 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.16   17.84     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 7768 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1208
       0.031 -    0.063: 484
       0.063 -    0.094: 139
       0.094 -    0.125: 133
       0.125 -    0.157: 9
  Chirality restraints: 1973
  Sorted by residual:
  chirality pdb=" CA  TRP B 252 "
            pdb=" N   TRP B 252 "
            pdb=" C   TRP B 252 "
            pdb=" CB  TRP B 252 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.14e-01
  chirality pdb=" CA  ASP A 333 "
            pdb=" N   ASP A 333 "
            pdb=" C   ASP A 333 "
            pdb=" CB  ASP A 333 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.91e-01
  chirality pdb=" CA  ILE A 998 "
            pdb=" N   ILE A 998 "
            pdb=" C   ILE A 998 "
            pdb=" CB  ILE A 998 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.47e-01
  ... (remaining 1970 not shown)

  Planarity restraints: 2259
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 252 "    0.023 2.00e-02 2.50e+03   2.52e-02 1.58e+01
        pdb=" CG  TRP B 252 "   -0.064 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 252 "    0.040 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 252 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 252 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 252 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 252 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 252 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 252 "    0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 252 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 493 "   -0.043 5.00e-02 4.00e+02   6.30e-02 6.35e+00
        pdb=" N   PRO A 494 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 494 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 494 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 332 "    0.012 2.00e-02 2.50e+03   2.45e-02 6.02e+00
        pdb=" C   TYR A 332 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   TYR A 332 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ASP A 333 "    0.014 2.00e-02 2.50e+03
  ... (remaining 2256 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1435
        2.75 -     3.29: 11692
        3.29 -     3.83: 21795
        3.83 -     4.36: 27795
        4.36 -     4.90: 47371
  Nonbonded interactions: 110088
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A1173 "
            pdb=" O   ILE A1212 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" NZ  LYS A 199 "
            pdb=" OE2 GLU B 364 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" NZ  LYS A1219 "
            pdb=" O   ILE C  11 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" OG  SER B 170 "
            pdb=" O   ASN B 172 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   ASN B 289 "
            pdb=" OG  SER B 307 "
     model   vdw
     2.234 3.040
  ... (remaining 110083 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:             1.150
  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:             0.020
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     16.100
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
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   0.076  13051  Z= 0.142
  Angle     :  0.569   7.844  17699  Z= 0.317
  Chirality :  0.044   0.157   1973
  Planarity :  0.004   0.063   2259
  Dihedral  : 13.137  88.585   4773
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.71 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.14 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.21), residues: 1571
  helix:  0.45 (0.58), residues: 93
  sheet:  0.23 (0.20), residues: 645
  loop : -0.97 (0.21), residues: 833

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 816 
 TYR   0.023   0.001   TYR A 938 
 PHE   0.018   0.001   PHE A1160 
 TRP   0.064   0.002   TRP B 252 
 HIS   0.005   0.001   HIS A 866 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (13047)
  covalent geometry    : angle       0.56894 (17696)
  hydrogen bonds       : bond        0.23008 (  429)
  hydrogen bonds       : angle       9.21536 ( 1116)
  metal coordination   : bond        0.00248 (    4)
  metal coordination   : angle       0.59154 (    3)

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

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

  3142 Ramachandran restraints generated.
    1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3142 Ramachandran restraints generated.
    1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 196
  time to evaluate  : 0.539 
Fit side-chains
   revert: symmetry clash
REVERT: B  246 ASP cc_start: 0.7575 (m-30) cc_final: 0.7325 (m-30)
  outliers start: 2
  outliers final: 1
  residues processed: 197
  average time/residue: 0.8331
  time to fit residues: 175.3973
Evaluate side-chains
  125 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    9 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 149 optimal weight:    2.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 477 ASN
A 648 GLN
** A 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1077 GLN
A1209 GLN
A1264 ASN
A1352 GLN
B  76 GLN
B 310 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.133449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.115257 restraints weight = 16770.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 1.60
r_work: 0.3312 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.1264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13051  Z= 0.193
  Angle     :  0.619   7.533  17699  Z= 0.324
  Chirality :  0.047   0.218   1973
  Planarity :  0.005   0.055   2259
  Dihedral  :  5.356  80.607   1734
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  4.90 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  :  9.90 %
    Favored  : 88.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.62 (0.21), residues: 1571
  helix:  0.30 (0.55), residues: 99
  sheet:  0.22 (0.20), residues: 643
  loop : -1.00 (0.21), residues: 829

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 702 
 TYR   0.010   0.001   TYR A 189 
 PHE   0.023   0.002   PHE A1160 
 TRP   0.021   0.002   TRP B 273 
 HIS   0.008   0.001   HIS A 866 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 (13047)
  covalent geometry    : angle       0.61910 (17696)
  hydrogen bonds       : bond        0.04790 (  429)
  hydrogen bonds       : angle       6.58063 ( 1116)
  metal coordination   : bond        0.00501 (    4)
  metal coordination   : angle       0.99472 (    3)

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

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

  3142 Ramachandran restraints generated.
    1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3142 Ramachandran restraints generated.
    1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 147
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 ARG cc_start: 0.7446 (ttp80) cc_final: 0.7186 (ttp80)
REVERT: A 1072 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7950 (mt-10)
REVERT: A 1199 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.6167 (tt0)
REVERT: C    1 MET cc_start: 0.5973 (tpt) cc_final: 0.5222 (tmm)
REVERT: B  246 ASP cc_start: 0.7798 (m-30) cc_final: 0.7422 (m-30)
REVERT: B  371 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7850 (tp30)
REVERT: B  372 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7932 (mpp)
  outliers start: 28
  outliers final: 5
  residues processed: 163
  average time/residue: 0.7916
  time to fit residues: 138.5888
Evaluate side-chains
  142 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 133
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  671 LYS
Chi-restraints excluded: chain A residue 1072 GLU
Chi-restraints excluded: chain A residue 1095 GLN
Chi-restraints excluded: chain A residue 1199 GLU
Chi-restraints excluded: chain A residue 1209 GLN
Chi-restraints excluded: chain B residue   77 ARG
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  371 GLU
Chi-restraints excluded: chain B residue  372 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 113 optimal weight:    1.9990
   chunk 83 optimal weight:    4.9990
   chunk 90 optimal weight:    0.6980
   chunk 152 optimal weight:    7.9990
   chunk 62 optimal weight:    7.9990
   chunk 91 optimal weight:    1.9990
   chunk 4 optimal weight:    7.9990
   chunk 34 optimal weight:    7.9990
   chunk 55 optimal weight:   10.0000
   chunk 18 optimal weight:    0.0870
   chunk 89 optimal weight:    0.9990
   overall best weight:    1.1564

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

Flipped N/Q/H residues before XYZ refinement:
A  29 ASN
** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 477 ASN
** A 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 991 ASN
A1077 GLN
A1209 GLN
A1264 ASN
B  60 ASN
B 310 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.134515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.116585 restraints weight = 16820.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 1.58
r_work: 0.3337 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.1416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13051  Z= 0.132
  Angle     :  0.559   8.326  17699  Z= 0.290
  Chirality :  0.045   0.178   1973
  Planarity :  0.004   0.070   2259
  Dihedral  :  4.817  21.231   1732
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.14 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 12.05 %
    Favored  : 86.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.64 (0.21), residues: 1571
  helix:  0.04 (0.54), residues: 105
  sheet:  0.19 (0.20), residues: 634
  loop : -0.95 (0.21), residues: 832

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 313 
 TYR   0.008   0.001   TYR A1356 
 PHE   0.013   0.001   PHE A1160 
 TRP   0.021   0.001   TRP B 273 
 HIS   0.007   0.001   HIS A 866 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (13047)
  covalent geometry    : angle       0.55846 (17696)
  hydrogen bonds       : bond        0.04032 (  429)
  hydrogen bonds       : angle       6.10579 ( 1116)
  metal coordination   : bond        0.00147 (    4)
  metal coordination   : angle       0.82715 (    3)

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

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

  3142 Ramachandran restraints generated.
    1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3142 Ramachandran restraints generated.
    1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 146
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 ARG cc_start: 0.7439 (ttp80) cc_final: 0.7040 (ttp80)
REVERT: A 1077 GLN cc_start: 0.8591 (mt0) cc_final: 0.7667 (mm-40)
REVERT: C    1 MET cc_start: 0.5776 (tpt) cc_final: 0.5169 (tmm)
REVERT: B  246 ASP cc_start: 0.7739 (m-30) cc_final: 0.7323 (m-30)
REVERT: B  372 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.7944 (mpp)
  outliers start: 27
  outliers final: 9
  residues processed: 159
  average time/residue: 0.7870
  time to fit residues: 134.4962
Evaluate side-chains
  144 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 134
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  477 ASN
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue 1095 GLN
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1209 GLN
Chi-restraints excluded: chain A residue 1417 GLU
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  323 GLU
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  375 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 126 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 146 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 26 optimal weight:    0.7980
   chunk 154 optimal weight:   10.0000
   chunk 158 optimal weight:    8.9990
   chunk 7 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   overall best weight:    2.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 991 ASN
A1209 GLN
** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1264 ASN
B 310 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.132059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.114065 restraints weight = 16878.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 1.58
r_work: 0.3294 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.1609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  13051  Z= 0.195
  Angle     :  0.604   9.187  17699  Z= 0.312
  Chirality :  0.046   0.185   1973
  Planarity :  0.004   0.081   2259
  Dihedral  :  5.026  22.533   1732
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.58 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 12.84 %
    Favored  : 84.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.70 (0.21), residues: 1571
  helix:  0.00 (0.53), residues: 105
  sheet:  0.12 (0.20), residues: 637
  loop : -0.97 (0.21), residues: 829

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 313 
 TYR   0.010   0.001   TYR A 701 
 PHE   0.017   0.002   PHE A1160 
 TRP   0.020   0.002   TRP B 273 
 HIS   0.007   0.001   HIS A 866 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (13047)
  covalent geometry    : angle       0.60346 (17696)
  hydrogen bonds       : bond        0.04231 (  429)
  hydrogen bonds       : angle       6.04978 ( 1116)
  metal coordination   : bond        0.00511 (    4)
  metal coordination   : angle       0.91781 (    3)

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

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

  3142 Ramachandran restraints generated.
    1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3142 Ramachandran restraints generated.
    1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 139
  time to evaluate  : 0.510 
Fit side-chains
REVERT: A  165 ARG cc_start: 0.7594 (ttp80) cc_final: 0.7050 (ttp80)
REVERT: A  870 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7284 (tt0)
REVERT: A 1199 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.6200 (tt0)
REVERT: A 1264 ASN cc_start: 0.7832 (t0) cc_final: 0.7613 (m110)
REVERT: A 1413 MET cc_start: 0.8403 (mmt) cc_final: 0.8132 (mmt)
REVERT: C    1 MET cc_start: 0.5713 (tpt) cc_final: 0.5410 (tmm)
REVERT: B  267 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8184 (mp10)
REVERT: B  372 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7955 (mpp)
  outliers start: 39
  outliers final: 8
  residues processed: 163
  average time/residue: 0.7895
  time to fit residues: 138.4180
Evaluate side-chains
  144 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  667 MET
Chi-restraints excluded: chain A residue  671 LYS
Chi-restraints excluded: chain A residue  870 GLU
Chi-restraints excluded: chain A residue 1029 VAL
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1199 GLU
Chi-restraints excluded: chain A residue 1209 GLN
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain B residue  372 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 118 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0170
   chunk 141 optimal weight:    8.9990
   chunk 121 optimal weight:   10.0000
   chunk 12 optimal weight:    0.9980
   chunk 78 optimal weight:    8.9990
   chunk 6 optimal weight:    0.9980
   chunk 130 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9990
   chunk 138 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    1.4022

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 691 HIS
** A 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 991 ASN
A1077 GLN
A1209 GLN
** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 189 GLN
B 310 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.133287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.115422 restraints weight = 16809.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 1.58
r_work: 0.3318 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.1698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  13051  Z= 0.143
  Angle     :  0.569   8.748  17699  Z= 0.293
  Chirality :  0.045   0.172   1973
  Planarity :  0.004   0.078   2259
  Dihedral  :  4.919  21.307   1732
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.20 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 14.20 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.68 (0.21), residues: 1571
  helix:  0.04 (0.54), residues: 105
  sheet:  0.12 (0.20), residues: 637
  loop : -0.94 (0.22), residues: 829

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 313 
 TYR   0.008   0.001   TYR A1356 
 PHE   0.013   0.001   PHE A 185 
 TRP   0.020   0.001   TRP B 273 
 HIS   0.007   0.001   HIS A 866 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (13047)
  covalent geometry    : angle       0.56904 (17696)
  hydrogen bonds       : bond        0.03791 (  429)
  hydrogen bonds       : angle       5.86131 ( 1116)
  metal coordination   : bond        0.00187 (    4)
  metal coordination   : angle       0.95736 (    3)

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

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

  3142 Ramachandran restraints generated.
    1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3142 Ramachandran restraints generated.
    1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 134
  time to evaluate  : 0.500 
Fit side-chains
REVERT: A  165 ARG cc_start: 0.7584 (ttp80) cc_final: 0.7010 (ttp80)
REVERT: A  870 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7275 (tt0)
REVERT: A 1199 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.6187 (tt0)
REVERT: C    1 MET cc_start: 0.5717 (tpt) cc_final: 0.5474 (tmm)
REVERT: B  267 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8166 (mp10)
REVERT: B  372 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7934 (mpp)
  outliers start: 28
  outliers final: 10
  residues processed: 152
  average time/residue: 0.7492
  time to fit residues: 122.9463
Evaluate side-chains
  140 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  667 MET
Chi-restraints excluded: chain A residue  870 GLU
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1167 GLU
Chi-restraints excluded: chain A residue 1199 GLU
Chi-restraints excluded: chain A residue 1209 GLN
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain B residue   58 ASP
Chi-restraints excluded: chain B residue   77 ARG
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  375 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 141 optimal weight:    8.9990
   chunk 79 optimal weight:    7.9990
   chunk 50 optimal weight:    9.9990
   chunk 44 optimal weight:    0.0980
   chunk 86 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 68 optimal weight:    8.9990
   chunk 136 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   chunk 112 optimal weight:    5.9990
   chunk 94 optimal weight:    3.9990
   overall best weight:    4.4188

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 477 ASN
A 615 ASN
** A 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1077 GLN
A1209 GLN
** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1264 ASN
** B  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 310 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.128176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.110113 restraints weight = 17038.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 1.59
r_work: 0.3236 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3135 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.061  13051  Z= 0.330
  Angle     :  0.710  11.101  17699  Z= 0.366
  Chirality :  0.051   0.183   1973
  Planarity :  0.005   0.078   2259
  Dihedral  :  5.548  25.578   1732
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.60 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 13.41 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.21), residues: 1571
  helix: -0.25 (0.51), residues: 105
  sheet: -0.05 (0.20), residues: 647
  loop : -1.10 (0.21), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 313 
 TYR   0.014   0.002   TYR A 155 
 PHE   0.019   0.002   PHE A1160 
 TRP   0.020   0.002   TRP B 273 
 HIS   0.007   0.001   HIS A 866 

Details of bonding type rmsd
  covalent geometry    : bond        0.00778 (13047)
  covalent geometry    : angle       0.70957 (17696)
  hydrogen bonds       : bond        0.04877 (  429)
  hydrogen bonds       : angle       6.32494 ( 1116)
  metal coordination   : bond        0.01056 (    4)
  metal coordination   : angle       1.09625 (    3)

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

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

  3142 Ramachandran restraints generated.
    1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3142 Ramachandran restraints generated.
    1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 133
  time to evaluate  : 0.550 
Fit side-chains
REVERT: A  858 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7787 (mt0)
REVERT: A  870 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7249 (tt0)
REVERT: A 1199 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6276 (tt0)
REVERT: A 1209 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7769 (mm-40)
REVERT: C    1 MET cc_start: 0.5678 (tpt) cc_final: 0.5268 (tmm)
REVERT: B  154 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8268 (mt-10)
REVERT: B  267 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8166 (mp10)
REVERT: B  371 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7856 (tp30)
REVERT: B  372 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7998 (mpp)
  outliers start: 53
  outliers final: 21
  residues processed: 169
  average time/residue: 0.7592
  time to fit residues: 138.6128
Evaluate side-chains
  160 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 131
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  260 SER
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  667 MET
Chi-restraints excluded: chain A residue  671 LYS
Chi-restraints excluded: chain A residue  709 THR
Chi-restraints excluded: chain A residue  858 GLN
Chi-restraints excluded: chain A residue  870 GLU
Chi-restraints excluded: chain A residue  949 SER
Chi-restraints excluded: chain A residue 1029 VAL
Chi-restraints excluded: chain A residue 1095 GLN
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1167 GLU
Chi-restraints excluded: chain A residue 1199 GLU
Chi-restraints excluded: chain A residue 1209 GLN
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain B residue   58 ASP
Chi-restraints excluded: chain B residue   77 ARG
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  154 GLU
Chi-restraints excluded: chain B residue  266 SER
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain B residue  371 GLU
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  375 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 62 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 112 optimal weight:    6.9990
   chunk 81 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 100 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1077 GLN
A1209 GLN
A1214 GLN
** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1264 ASN
** B  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 310 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.132268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.114459 restraints weight = 16703.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 1.59
r_work: 0.3301 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13051  Z= 0.140
  Angle     :  0.584   9.330  17699  Z= 0.299
  Chirality :  0.045   0.165   1973
  Planarity :  0.004   0.074   2259
  Dihedral  :  5.110  21.908   1732
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.46 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 15.06 %
    Favored  : 82.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.79 (0.21), residues: 1571
  helix: -0.04 (0.53), residues: 105
  sheet:  0.02 (0.20), residues: 633
  loop : -1.00 (0.22), residues: 833

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 313 
 TYR   0.011   0.001   TYR A1120 
 PHE   0.017   0.001   PHE A 185 
 TRP   0.022   0.001   TRP B 273 
 HIS   0.007   0.001   HIS A 866 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (13047)
  covalent geometry    : angle       0.58393 (17696)
  hydrogen bonds       : bond        0.03751 (  429)
  hydrogen bonds       : angle       5.92833 ( 1116)
  metal coordination   : bond        0.00079 (    4)
  metal coordination   : angle       1.08656 (    3)

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

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

  3142 Ramachandran restraints generated.
    1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3142 Ramachandran restraints generated.
    1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 136
  time to evaluate  : 0.551 
Fit side-chains
REVERT: A  165 ARG cc_start: 0.7691 (ttp80) cc_final: 0.6968 (ttp-110)
REVERT: A  870 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7262 (tt0)
REVERT: A 1199 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6217 (tt0)
REVERT: A 1209 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7547 (mm-40)
REVERT: A 1264 ASN cc_start: 0.7849 (t0) cc_final: 0.7633 (m110)
REVERT: A 1427 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7694 (p0)
REVERT: C    1 MET cc_start: 0.5585 (tpt) cc_final: 0.5314 (tmm)
REVERT: B  267 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8150 (mp10)
REVERT: B  372 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7873 (mpp)
  outliers start: 35
  outliers final: 12
  residues processed: 156
  average time/residue: 0.7618
  time to fit residues: 128.1684
Evaluate side-chains
  147 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 SER
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  667 MET
Chi-restraints excluded: chain A residue  870 GLU
Chi-restraints excluded: chain A residue 1029 VAL
Chi-restraints excluded: chain A residue 1095 GLN
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1167 GLU
Chi-restraints excluded: chain A residue 1199 GLU
Chi-restraints excluded: chain A residue 1209 GLN
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1427 ASP
Chi-restraints excluded: chain B residue   58 ASP
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  375 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 141 optimal weight:    7.9990
   chunk 158 optimal weight:    8.9990
   chunk 57 optimal weight:    1.9990
   chunk 117 optimal weight:   10.0000
   chunk 116 optimal weight:    3.9990
   chunk 147 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1077 GLN
A1209 GLN
A1214 GLN
** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 310 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.130363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.112442 restraints weight = 16816.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 1.59
r_work: 0.3272 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  13051  Z= 0.214
  Angle     :  0.628   9.886  17699  Z= 0.322
  Chirality :  0.047   0.178   1973
  Planarity :  0.004   0.072   2259
  Dihedral  :  5.242  23.072   1732
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.22 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 15.21 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.84 (0.21), residues: 1571
  helix: -0.09 (0.53), residues: 105
  sheet: -0.01 (0.20), residues: 636
  loop : -1.03 (0.22), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 313 
 TYR   0.010   0.002   TYR A1356 
 PHE   0.018   0.002   PHE B 143 
 TRP   0.020   0.002   TRP B 273 
 HIS   0.006   0.001   HIS A 866 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 (13047)
  covalent geometry    : angle       0.62774 (17696)
  hydrogen bonds       : bond        0.04134 (  429)
  hydrogen bonds       : angle       6.01427 ( 1116)
  metal coordination   : bond        0.00439 (    4)
  metal coordination   : angle       1.08030 (    3)

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

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

  3142 Ramachandran restraints generated.
    1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3142 Ramachandran restraints generated.
    1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 127
  time to evaluate  : 0.546 
Fit side-chains
REVERT: A  165 ARG cc_start: 0.7743 (ttp80) cc_final: 0.6920 (ttp-110)
REVERT: A  258 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8029 (mp)
REVERT: A  870 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7266 (tt0)
REVERT: A 1093 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7507 (mp0)
REVERT: A 1199 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.6236 (tt0)
REVERT: A 1427 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7686 (p0)
REVERT: C    1 MET cc_start: 0.5644 (tpt) cc_final: 0.5298 (tmm)
REVERT: B  267 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8125 (mp10)
REVERT: B  372 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7945 (mpp)
  outliers start: 40
  outliers final: 15
  residues processed: 153
  average time/residue: 0.7692
  time to fit residues: 126.7855
Evaluate side-chains
  148 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  260 SER
Chi-restraints excluded: chain A residue  667 MET
Chi-restraints excluded: chain A residue  870 GLU
Chi-restraints excluded: chain A residue 1029 VAL
Chi-restraints excluded: chain A residue 1093 GLU
Chi-restraints excluded: chain A residue 1095 GLN
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1167 GLU
Chi-restraints excluded: chain A residue 1199 GLU
Chi-restraints excluded: chain A residue 1209 GLN
Chi-restraints excluded: chain A residue 1384 LEU
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1427 ASP
Chi-restraints excluded: chain B residue   58 ASP
Chi-restraints excluded: chain B residue   91 ASP
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  266 SER
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  375 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 85 optimal weight:    6.9990
   chunk 77 optimal weight:    0.5980
   chunk 24 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 135 optimal weight:    8.9990
   chunk 66 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 105 optimal weight:    0.0980
   chunk 8 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 144 optimal weight:    0.7980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1077 GLN
A1209 GLN
A1214 GLN
** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1264 ASN
B 310 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.133493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.115814 restraints weight = 16827.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 1.58
r_work: 0.3324 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13051  Z= 0.120
  Angle     :  0.563   9.914  17699  Z= 0.289
  Chirality :  0.045   0.171   1973
  Planarity :  0.004   0.073   2259
  Dihedral  :  4.916  21.198   1732
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.71 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 16.14 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.74 (0.21), residues: 1571
  helix:  0.07 (0.54), residues: 105
  sheet:  0.05 (0.20), residues: 636
  loop : -0.96 (0.22), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 313 
 TYR   0.010   0.001   TYR A1120 
 PHE   0.017   0.001   PHE A 185 
 TRP   0.022   0.001   TRP B 273 
 HIS   0.006   0.001   HIS A 866 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (13047)
  covalent geometry    : angle       0.56297 (17696)
  hydrogen bonds       : bond        0.03451 (  429)
  hydrogen bonds       : angle       5.71106 ( 1116)
  metal coordination   : bond        0.00237 (    4)
  metal coordination   : angle       1.06221 (    3)

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

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

  3142 Ramachandran restraints generated.
    1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3142 Ramachandran restraints generated.
    1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 ARG cc_start: 0.7673 (ttp80) cc_final: 0.7315 (ttp80)
REVERT: A  258 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7957 (mp)
REVERT: A  870 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7263 (tt0)
REVERT: A 1093 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7467 (mp0)
REVERT: A 1199 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.6188 (tt0)
REVERT: A 1209 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7986 (mp10)
REVERT: A 1395 VAL cc_start: 0.7064 (OUTLIER) cc_final: 0.6820 (p)
REVERT: C    1 MET cc_start: 0.5588 (tpt) cc_final: 0.5355 (tmt)
REVERT: B  267 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8144 (mp10)
REVERT: B  372 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7842 (mpp)
  outliers start: 28
  outliers final: 8
  residues processed: 154
  average time/residue: 0.8015
  time to fit residues: 132.7295
Evaluate side-chains
  141 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 HIS
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  667 MET
Chi-restraints excluded: chain A residue  870 GLU
Chi-restraints excluded: chain A residue 1029 VAL
Chi-restraints excluded: chain A residue 1093 GLU
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1167 GLU
Chi-restraints excluded: chain A residue 1199 GLU
Chi-restraints excluded: chain A residue 1209 GLN
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain A residue 1417 GLU
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  375 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 151 optimal weight:    5.9990
   chunk 121 optimal weight:    8.9990
   chunk 152 optimal weight:    0.8980
   chunk 79 optimal weight:    3.9990
   chunk 37 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 84 optimal weight:    5.9990
   chunk 46 optimal weight:    8.9990
   chunk 66 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1077 GLN
A1209 GLN
A1214 GLN
** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 310 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.129645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.111728 restraints weight = 16998.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 1.59
r_work: 0.3261 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  13051  Z= 0.249
  Angle     :  0.663  10.214  17699  Z= 0.340
  Chirality :  0.048   0.184   1973
  Planarity :  0.005   0.070   2259
  Dihedral  :  5.328  23.495   1732
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.60 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.57 %
    Favored  : 81.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.86 (0.21), residues: 1571
  helix: -0.10 (0.53), residues: 105
  sheet: -0.05 (0.20), residues: 649
  loop : -1.03 (0.22), residues: 817

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 313 
 TYR   0.011   0.002   TYR A 396 
 PHE   0.024   0.002   PHE B 143 
 TRP   0.019   0.002   TRP B 273 
 HIS   0.006   0.001   HIS A 866 

Details of bonding type rmsd
  covalent geometry    : bond        0.00586 (13047)
  covalent geometry    : angle       0.66258 (17696)
  hydrogen bonds       : bond        0.04347 (  429)
  hydrogen bonds       : angle       6.03069 ( 1116)
  metal coordination   : bond        0.00581 (    4)
  metal coordination   : angle       1.12816 (    3)

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

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

  3142 Ramachandran restraints generated.
    1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3142 Ramachandran restraints generated.
    1571 Oldfield, 0 Emsley, 1571 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 127
  time to evaluate  : 0.572 
Fit side-chains
REVERT: A   63 ARG cc_start: 0.6452 (mmp80) cc_final: 0.6121 (mmp80)
REVERT: A  165 ARG cc_start: 0.7779 (ttp80) cc_final: 0.6919 (ttp-110)
REVERT: A  258 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8078 (mp)
REVERT: A  616 ARG cc_start: 0.7830 (ttt-90) cc_final: 0.7526 (ttt90)
REVERT: A  870 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7224 (tt0)
REVERT: A 1093 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7475 (mp0)
REVERT: A 1199 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.6244 (tt0)
REVERT: A 1209 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7617 (mm-40)
REVERT: C    1 MET cc_start: 0.5693 (tpt) cc_final: 0.5055 (tmm)
REVERT: B  267 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8176 (mp10)
REVERT: B  372 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7982 (mpp)
  outliers start: 27
  outliers final: 12
  residues processed: 147
  average time/residue: 0.8057
  time to fit residues: 127.4152
Evaluate side-chains
  147 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  252 HIS
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  667 MET
Chi-restraints excluded: chain A residue  870 GLU
Chi-restraints excluded: chain A residue 1029 VAL
Chi-restraints excluded: chain A residue 1093 GLU
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1167 GLU
Chi-restraints excluded: chain A residue 1199 GLU
Chi-restraints excluded: chain A residue 1209 GLN
Chi-restraints excluded: chain A residue 1395 VAL
Chi-restraints excluded: chain B residue   58 ASP
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  266 SER
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  375 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 131 optimal weight:    3.9990
   chunk 123 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 148 optimal weight:    1.9990
   chunk 104 optimal weight:    5.9990
   chunk 142 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 110 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 87 optimal weight:    4.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1077 GLN
A1209 GLN
A1214 GLN
** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 310 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.131225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.113355 restraints weight = 16785.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 1.59
r_work: 0.3286 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3188 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.2043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  13051  Z= 0.177
  Angle     :  0.611  10.121  17699  Z= 0.313
  Chirality :  0.046   0.176   1973
  Planarity :  0.004   0.072   2259
  Dihedral  :  5.187  22.068   1732
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.22 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 16.86 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.84 (0.21), residues: 1571
  helix: -0.12 (0.53), residues: 105
  sheet: -0.02 (0.20), residues: 635
  loop : -1.02 (0.22), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 313 
 TYR   0.011   0.001   TYR A 617 
 PHE   0.021   0.002   PHE B 143 
 TRP   0.021   0.002   TRP B 273 
 HIS   0.006   0.001   HIS A 866 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 (13047)
  covalent geometry    : angle       0.61098 (17696)
  hydrogen bonds       : bond        0.03902 (  429)
  hydrogen bonds       : angle       5.92301 ( 1116)
  metal coordination   : bond        0.00085 (    4)
  metal coordination   : angle       1.08002 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4445.21 seconds
wall clock time: 77 minutes 7.00 seconds (4627.00 seconds total)