Starting phenix.real_space_refine
on Thu May 15 05:24:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y5q_33622/05_2025/7y5q_33622_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y5q_33622/05_2025/7y5q_33622.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y5q_33622/05_2025/7y5q_33622.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y5q_33622/05_2025/7y5q_33622.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y5q_33622/05_2025/7y5q_33622_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y5q_33622/05_2025/7y5q_33622_neut.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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     114      5.16       5
     C    7987      2.51       5
     N    2216      2.21       5
     O    2444      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 12762
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2919
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 380, 2919
          Classifications: {'peptide': 380}
          Link IDs: {'PTRANS': 28, 'TRANS': 351}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 8501
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1082, 8501
          Classifications: {'peptide': 1082}
          Link IDs: {'PTRANS': 67, 'TRANS': 1014}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 1341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 1341
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 2, 'TRANS': 169}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.55, per 1000 atoms: 0.59
  Number of scatterers: 12762
  At special positions: 0
  Unit cell: (114.995, 114.995, 139.26, 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     114     16.00
     O    2444      8.00
     N    2216      7.00
     C    7987      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=42, symmetry=0
    Simple disulfide: pdb=" SG  CYS A1135 " - pdb=" SG  CYS A1189 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1147 " - pdb=" SG  CYS A1158 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1162 " - pdb=" SG  CYS A1200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1205 " - pdb=" SG  CYS A1249 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1220 " - pdb=" SG  CYS A1230 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1234 " - pdb=" SG  CYS A1262 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1266 " - pdb=" SG  CYS A1319 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1282 " - pdb=" SG  CYS A1293 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1297 " - pdb=" SG  CYS A1330 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1335 " - pdb=" SG  CYS A1378 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1348 " - pdb=" SG  CYS A1358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1412 " - pdb=" SG  CYS A1422 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1426 " - pdb=" SG  CYS A1474 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1478 " - pdb=" SG  CYS A1496 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1487 " - pdb=" SG  CYS A1503 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1504 " - pdb=" SG  CYS A1528 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1520 " - pdb=" SG  CYS A1526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  64 " - pdb=" SG  CYS B 155 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 247 " - pdb=" SG  CYS B 507 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 252 " - pdb=" SG  CYS B 577 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 334 " - pdb=" SG  CYS B 348 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 344 " - pdb=" SG  CYS B 360 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 394 " - pdb=" SG  CYS B 405 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 503 " - pdb=" SG  CYS B 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 532 " - pdb=" SG  CYS B 563 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 630 " - pdb=" SG  CYS B 801 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 633 " - pdb=" SG  CYS B 798 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 652 " - pdb=" SG  CYS C 120 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 673 " - pdb=" SG  CYS B 755 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 695 " - pdb=" SG  CYS B 701 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 867 " - pdb=" SG  CYS B 895 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 880 " - pdb=" SG  CYS B 891 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 903 " - pdb=" SG  CYS B 910 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 919 " - pdb=" SG  CYS B 931 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 956 " - pdb=" SG  CYS B 990 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 971 " - pdb=" SG  CYS B1059 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  56 " - pdb=" SG  CYS C  70 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  65 " - pdb=" SG  CYS C  85 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  76 " - pdb=" SG  CYS C 125 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 109 " - pdb=" SG  CYS C 139 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 146 " - pdb=" SG  CYS C 181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 197 " - pdb=" SG  CYS C 205 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.19
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B1601 "
        pdb="ZN    ZN B1601 " - pdb=" NE2 HIS B 486 "
        pdb="ZN    ZN B1601 " - pdb=" NE2 HIS B 482 "
        pdb="ZN    ZN B1601 " - pdb=" NE2 HIS B 492 "


  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3048

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 22 sheets defined
      17.9% alpha, 18.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1279 through 1284
      removed outlier: 3.715A  pdb=" N   ARG A1283 " --> pdb=" O   ALA A1280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1496 through 1501
      removed outlier: 4.221A  pdb=" N   GLY A1500 " --> pdb=" O   CYS A1496 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLY A1501 " --> pdb=" O   ASN A1497 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1496 through 1501'
    Processing helix  chain 'A' and resid 1504 through 1508
    Processing helix  chain 'B' and resid 184 through 195
      removed outlier: 3.683A  pdb=" N   GLU B 193 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 216
      removed outlier: 4.366A  pdb=" N   ALA B 216 " --> pdb=" O   ASN B 212 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 212 through 216'
    Processing helix  chain 'B' and resid 250 through 253
      removed outlier: 3.564A  pdb=" N   ASP B 253 " --> pdb=" O   THR B 250 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 250 through 253'
    Processing helix  chain 'B' and resid 254 through 259
    Processing helix  chain 'B' and resid 259 through 264
      removed outlier: 3.736A  pdb=" N   LEU B 264 " --> pdb=" O   SER B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 305
      removed outlier: 3.613A  pdb=" N   HIS B 300 " --> pdb=" O   ASP B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 309
    Processing helix  chain 'B' and resid 322 through 327
      removed outlier: 3.634A  pdb=" N   ARG B 327 " --> pdb=" O   SER B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 336 through 341
      removed outlier: 4.031A  pdb=" N   GLY B 340 " --> pdb=" O   ILE B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 358
    Processing helix  chain 'B' and resid 400 through 405
      removed outlier: 4.168A  pdb=" N   THR B 404 " --> pdb=" O   ASN B 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 426
      removed outlier: 3.546A  pdb=" N   ASN B 423 " --> pdb=" O   ASN B 419 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 478 through 488
      removed outlier: 3.591A  pdb=" N   GLU B 483 " --> pdb=" O   THR B 479 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 492 through 496
      removed outlier: 4.391A  pdb=" N   GLY B 496 " --> pdb=" O   VAL B 493 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 571 through 576
      removed outlier: 3.703A  pdb=" N   MET B 575 " --> pdb=" O   GLN B 571 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 577 through 582
    Processing helix  chain 'B' and resid 815 through 820
      removed outlier: 3.688A  pdb=" N   SER B 820 " --> pdb=" O   MET B 816 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 873 through 877
    Processing helix  chain 'B' and resid 921 through 925
      removed outlier: 3.803A  pdb=" N   GLN B 924 " --> pdb=" O   GLU B 921 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   LYS B 925 " --> pdb=" O   PHE B 922 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 921 through 925'
    Processing helix  chain 'B' and resid 958 through 962
      removed outlier: 4.216A  pdb=" N   ILE B 961 " --> pdb=" O   GLY B 958 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ILE B 962 " --> pdb=" O   TRP B 959 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 958 through 962'
    Processing helix  chain 'B' and resid 993 through 1001
      removed outlier: 3.620A  pdb=" N   GLN B1001 " --> pdb=" O   SER B 997 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 49 through 60
    Processing helix  chain 'C' and resid 65 through 72
    Processing helix  chain 'C' and resid 80 through 89
    Processing helix  chain 'C' and resid 96 through 118
    Processing helix  chain 'C' and resid 124 through 142
      removed outlier: 3.690A  pdb=" N   LYS C 142 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 152
      removed outlier: 3.685A  pdb=" N   ASN C 152 " --> pdb=" O   ALA C 148 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 152 through 158
      removed outlier: 3.900A  pdb=" N   ILE C 156 " --> pdb=" O   ASN C 152 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 161 through 166
    Processing helix  chain 'C' and resid 168 through 179
    Processing helix  chain 'C' and resid 182 through 201
      removed outlier: 3.615A  pdb=" N   GLU C 198 " --> pdb=" O   GLN C 194 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 208
      removed outlier: 3.801A  pdb=" N   SER C 206 " --> pdb=" O   GLY C 202 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1143 through 1144
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1169 through 1172
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1189 through 1190
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1216 through 1219
      removed outlier: 3.592A  pdb=" N   SER A1231 " --> pdb=" O   SER A1219 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1238 through 1241
      removed outlier: 3.603A  pdb=" N   LYS A1241 " --> pdb=" O   LEU A1261 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1275 through 1277
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1301 through 1302
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1431 through 1435
    Processing sheet with id=AA9, first strand: chain 'B' and resid 135 through 140
      removed outlier: 6.983A  pdb=" N   LEU B 130 " --> pdb=" O   VAL B 137 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   THR B 139 " --> pdb=" O   MET B 128 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   MET B 128 " --> pdb=" O   THR B 139 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 135 through 140
      removed outlier: 6.983A  pdb=" N   LEU B 130 " --> pdb=" O   VAL B 137 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   THR B 139 " --> pdb=" O   MET B 128 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   MET B 128 " --> pdb=" O   THR B 139 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   LYS B 227 " --> pdb=" O   TYR B  18 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 103 through 105
      removed outlier: 6.742A  pdb=" N   TRP B  73 " --> pdb=" O   GLY B  59 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   GLY B  59 " --> pdb=" O   TRP B  73 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   VAL B  75 " --> pdb=" O   ILE B  57 " (cutoff:3.500A)
      removed outlier: 5.283A  pdb=" N   LEU B 158 " --> pdb=" O   LEU B  28 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LEU B 160 " --> pdb=" O   LEU B  26 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 311 through 321
      removed outlier: 3.692A  pdb=" N   VAL B 277 " --> pdb=" O   ASP B 316 " (cutoff:3.500A)
      removed outlier: 5.049A  pdb=" N   PHE B 437 " --> pdb=" O   VAL B 278 " (cutoff:3.500A)
      removed outlier: 8.441A  pdb=" N   LEU B 280 " --> pdb=" O   PHE B 437 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 329 through 331
    Processing sheet with id=AB5, first strand: chain 'B' and resid 600 through 604
      removed outlier: 4.960A  pdb=" N   VAL B 601 " --> pdb=" O   GLU B 612 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   GLU B 612 " --> pdb=" O   VAL B 601 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLY B 603 " --> pdb=" O   THR B 610 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL B 609 " --> pdb=" O   ASP B 830 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ASP B 830 " --> pdb=" O   VAL B 609 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 640 through 642
      removed outlier: 3.689A  pdb=" N   GLN B 641 " --> pdb=" O   LEU B 789 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   GLU B 783 " --> pdb=" O   THR B 721 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   TRP B 719 " --> pdb=" O   ASP B 785 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   ALA B 787 " --> pdb=" O   THR B 717 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   THR B 717 " --> pdb=" O   ALA B 787 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   LEU B 789 " --> pdb=" O   SER B 715 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   SER B 715 " --> pdb=" O   LEU B 789 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   SER B 791 " --> pdb=" O   PRO B 713 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 645 through 647
      removed outlier: 6.197A  pdb=" N   TYR B 771 " --> pdb=" O   PHE B 707 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 690 through 691
      removed outlier: 4.006A  pdb=" N   ILE C 121 " --> pdb=" O   VAL B 691 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 805 through 810
    Processing sheet with id=AC1, first strand: chain 'B' and resid 902 through 903
    Processing sheet with id=AC2, first strand: chain 'B' and resid 939 through 943
      removed outlier: 4.045A  pdb=" N   ILE B1020 " --> pdb=" O   ALA B1097 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 948 through 949
    Processing sheet with id=AC4, first strand: chain 'B' and resid 948 through 949

    318 hydrogen bonds defined for protein.
    846 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: 5.10

  Time building geometry restraints manager: 3.65 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4112
        1.34 -     1.46: 2628
        1.46 -     1.58: 6209
        1.58 -     1.70: 0
        1.70 -     1.82: 139
  Bond restraints: 13088
  Sorted by residual:
  bond pdb=" N   ASN B1062 "
       pdb=" CA  ASN B1062 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.033 1.04e-02 9.25e+03 1.04e+01
  bond pdb=" N   HIS A1236 "
       pdb=" CA  HIS A1236 "
    ideal  model  delta    sigma   weight residual
    1.461  1.490 -0.029 9.20e-03 1.18e+04 1.00e+01
  bond pdb=" N   PHE A1516 "
       pdb=" CA  PHE A1516 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.04e-02 9.25e+03 8.62e+00
  bond pdb=" N   ILE C 160 "
       pdb=" CA  ILE C 160 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.19e-02 7.06e+03 8.19e+00
  bond pdb=" N   CYS A1520 "
       pdb=" CA  CYS A1520 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.31e-02 5.83e+03 8.16e+00
  ... (remaining 13083 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 17264
        1.77 -     3.54: 464
        3.54 -     5.31: 51
        5.31 -     7.08: 9
        7.08 -     8.85: 8
  Bond angle restraints: 17796
  Sorted by residual:
  angle pdb=" N   TRP A1465 "
        pdb=" CA  TRP A1465 "
        pdb=" C   TRP A1465 "
      ideal   model   delta    sigma   weight residual
     112.88  106.11    6.77 1.29e+00 6.01e-01 2.75e+01
  angle pdb=" N   LEU C  45 "
        pdb=" CA  LEU C  45 "
        pdb=" C   LEU C  45 "
      ideal   model   delta    sigma   weight residual
     113.02  107.88    5.14 1.20e+00 6.94e-01 1.83e+01
  angle pdb=" N   ASN B1061 "
        pdb=" CA  ASN B1061 "
        pdb=" C   ASN B1061 "
      ideal   model   delta    sigma   weight residual
     111.55  105.70    5.85 1.37e+00 5.33e-01 1.82e+01
  angle pdb=" N   GLU C 158 "
        pdb=" CA  GLU C 158 "
        pdb=" C   GLU C 158 "
      ideal   model   delta    sigma   weight residual
     112.93  108.40    4.53 1.12e+00 7.97e-01 1.64e+01
  angle pdb=" CA  TYR A1466 "
        pdb=" C   TYR A1466 "
        pdb=" N   PRO A1467 "
      ideal   model   delta    sigma   weight residual
     117.60  122.26   -4.66 1.18e+00 7.18e-01 1.56e+01
  ... (remaining 17791 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 7186
       17.92 -    35.84: 603
       35.84 -    53.76: 118
       53.76 -    71.68: 21
       71.68 -    89.59: 5
  Dihedral angle restraints: 7933
    sinusoidal: 3205
      harmonic: 4728
  Sorted by residual:
  dihedral pdb=" CB  CYS C 109 "
           pdb=" SG  CYS C 109 "
           pdb=" SG  CYS C 139 "
           pdb=" CB  CYS C 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  159.33  -66.33     1      1.00e+01 1.00e-02 5.75e+01
  dihedral pdb=" CB  CYS B 956 "
           pdb=" SG  CYS B 956 "
           pdb=" SG  CYS B 990 "
           pdb=" CB  CYS B 990 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  150.97  -57.97     1      1.00e+01 1.00e-02 4.51e+01
  dihedral pdb=" CB  CYS B 867 "
           pdb=" SG  CYS B 867 "
           pdb=" SG  CYS B 895 "
           pdb=" CB  CYS B 895 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -142.60   56.60     1      1.00e+01 1.00e-02 4.32e+01
  ... (remaining 7930 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 1590
       0.064 -    0.128: 298
       0.128 -    0.192: 32
       0.192 -    0.256: 3
       0.256 -    0.319: 3
  Chirality restraints: 1926
  Sorted by residual:
  chirality pdb=" CA  TYR A1466 "
            pdb=" N   TYR A1466 "
            pdb=" C   TYR A1466 "
            pdb=" CB  TYR A1466 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.55e+00
  chirality pdb=" CA  PHE A1516 "
            pdb=" N   PHE A1516 "
            pdb=" C   PHE A1516 "
            pdb=" CB  PHE A1516 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 2.02e+00
  chirality pdb=" CA  LEU A1463 "
            pdb=" N   LEU A1463 "
            pdb=" C   LEU A1463 "
            pdb=" CB  LEU A1463 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.87e+00
  ... (remaining 1923 not shown)

  Planarity restraints: 2346
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B1060 "    0.015 2.00e-02 2.50e+03   2.93e-02 8.60e+00
        pdb=" C   ARG B1060 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   ARG B1060 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ASN B1061 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A1234 "    0.011 2.00e-02 2.50e+03   2.27e-02 5.14e+00
        pdb=" C   CYS A1234 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   CYS A1234 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ARG A1235 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 687 "   -0.037 5.00e-02 4.00e+02   5.66e-02 5.12e+00
        pdb=" N   PRO B 688 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO B 688 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 688 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 2343 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 4020
        2.83 -     3.35: 10557
        3.35 -     3.87: 20341
        3.87 -     4.38: 22501
        4.38 -     4.90: 39879
  Nonbonded interactions: 97298
  Sorted by model distance:
  nonbonded pdb=" O   GLY A1501 "
            pdb=" OG1 THR A1507 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" OD2 ASP B 830 "
            pdb=" OH  TYR B 841 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" OG  SER B 675 "
            pdb=" OE2 GLU B 783 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" OG1 THR B 541 "
            pdb=" O   PHE B 544 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" OG1 THR A1320 "
            pdb=" O   SER A1324 "
     model   vdw
     2.331 3.040
  ... (remaining 97293 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.560
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     33.870
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.060
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   38.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  13133  Z= 0.243
  Angle     :  0.683   8.855  17880  Z= 0.400
  Chirality :  0.051   0.319   1926
  Planarity :  0.006   0.057   2346
  Dihedral  : 13.443  89.594   4759
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  6.70 %
    Allowed  :  8.09 %
    Favored  : 85.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.19), residues: 1620
  helix: -2.78 (0.23), residues: 248
  sheet: -0.66 (0.32), residues: 296
  loop : -1.33 (0.18), residues: 1076

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  44 
 HIS   0.004   0.001   HIS B  78 
 PHE   0.021   0.002   PHE B 912 
 TYR   0.013   0.002   TYR B 169 
 ARG   0.002   0.000   ARG C 115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25364 (  303)
  hydrogen bonds       : angle       9.33765 (  846)
  metal coordination   : bond        0.00296 (    3)
  SS BOND              : bond        0.00330 (   42)
  SS BOND              : angle       1.03428 (   84)
  covalent geometry    : bond        0.00457 (13088)
  covalent geometry    : angle       0.68115 (17796)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 96
    poor density    : 199
  time to evaluate  : 1.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1152 ARG cc_start: 0.6819 (mpt-90) cc_final: 0.6025 (mmt-90)
REVERT: A 1169 GLN cc_start: 0.7498 (mp10) cc_final: 0.7134 (mm-40)
REVERT: A 1466 TYR cc_start: 0.2577 (OUTLIER) cc_final: 0.2338 (m-80)
REVERT: A 1479 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.5909 (tp30)
REVERT: B   71 ARG cc_start: 0.9030 (mmt180) cc_final: 0.8691 (mmt180)
REVERT: B  112 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8076 (mm)
REVERT: B  174 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8122 (tm-30)
REVERT: B  246 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7247 (mm)
REVERT: B  293 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7669 (pp20)
REVERT: B  407 ASP cc_start: 0.6874 (m-30) cc_final: 0.6577 (m-30)
REVERT: B  479 THR cc_start: 0.9042 (t) cc_final: 0.8758 (m)
REVERT: B  481 ILE cc_start: 0.9155 (mm) cc_final: 0.8955 (mm)
REVERT: B  959 TRP cc_start: 0.6820 (p-90) cc_final: 0.6493 (p-90)
REVERT: B  988 TYR cc_start: 0.7529 (p90) cc_final: 0.7210 (p90)
REVERT: C   47 LEU cc_start: 0.4630 (OUTLIER) cc_final: 0.4227 (tp)
REVERT: C  210 PHE cc_start: 0.5015 (OUTLIER) cc_final: 0.4632 (t80)
  outliers start: 96
  outliers final: 34
  residues processed: 271
  average time/residue: 0.2347
  time to fit residues: 93.0788
Evaluate side-chains
  191 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 149
  time to evaluate  : 1.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1188 THR
Chi-restraints excluded: chain A residue 1207 ILE
Chi-restraints excluded: chain A residue 1282 CYS
Chi-restraints excluded: chain A residue 1317 THR
Chi-restraints excluded: chain A residue 1320 THR
Chi-restraints excluded: chain A residue 1410 LEU
Chi-restraints excluded: chain A residue 1412 CYS
Chi-restraints excluded: chain A residue 1458 VAL
Chi-restraints excluded: chain A residue 1466 TYR
Chi-restraints excluded: chain A residue 1479 GLU
Chi-restraints excluded: chain A residue 1514 THR
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  174 GLU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  293 GLU
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain B residue  550 THR
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  717 THR
Chi-restraints excluded: chain B residue  727 TRP
Chi-restraints excluded: chain B residue  808 VAL
Chi-restraints excluded: chain B residue  809 VAL
Chi-restraints excluded: chain B residue  845 THR
Chi-restraints excluded: chain B residue  882 ASP
Chi-restraints excluded: chain B residue  918 VAL
Chi-restraints excluded: chain B residue  940 LEU
Chi-restraints excluded: chain B residue 1004 PHE
Chi-restraints excluded: chain B residue 1078 HIS
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  135 LEU
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  197 CYS
Chi-restraints excluded: chain C residue  210 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 137 optimal weight:    5.9990
   chunk 123 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 66 optimal weight:    0.5980
   chunk 127 optimal weight:    7.9990
   chunk 49 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 95 optimal weight:    0.7980
   chunk 148 optimal weight:    3.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
A1142 ASN
A1236 HIS
** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 175 HIS
B 232 ASN
B 294 GLN
B 298 GLN
** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 774 GLN
B 834 ASN
** C  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  82 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.169123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.144486 restraints weight = 16696.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.140683 restraints weight = 27536.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.139155 restraints weight = 25899.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.1228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13133  Z= 0.161
  Angle     :  0.577   7.378  17880  Z= 0.305
  Chirality :  0.044   0.173   1926
  Planarity :  0.005   0.043   2346
  Dihedral  :  7.764  59.729   1814
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 13.05 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.20), residues: 1620
  helix: -1.58 (0.30), residues: 246
  sheet: -0.73 (0.30), residues: 325
  loop : -1.06 (0.19), residues: 1049

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 179 
 HIS   0.007   0.001   HIS B  78 
 PHE   0.018   0.002   PHE B  91 
 TYR   0.014   0.001   TYR A1498 
 ARG   0.004   0.000   ARG B 292 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04699 (  303)
  hydrogen bonds       : angle       6.31287 (  846)
  metal coordination   : bond        0.00270 (    3)
  SS BOND              : bond        0.00332 (   42)
  SS BOND              : angle       1.30734 (   84)
  covalent geometry    : bond        0.00376 (13088)
  covalent geometry    : angle       0.57162 (17796)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 164
  time to evaluate  : 1.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1169 GLN cc_start: 0.7513 (mp10) cc_final: 0.7048 (mm-40)
REVERT: A 1384 TRP cc_start: 0.3479 (OUTLIER) cc_final: 0.3090 (m-90)
REVERT: A 1479 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.5895 (tp30)
REVERT: B  112 LEU cc_start: 0.8288 (mm) cc_final: 0.8063 (mm)
REVERT: B  246 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7427 (mm)
REVERT: B  407 ASP cc_start: 0.7005 (m-30) cc_final: 0.6634 (m-30)
REVERT: B  412 HIS cc_start: 0.5566 (OUTLIER) cc_final: 0.5114 (p90)
REVERT: B  479 THR cc_start: 0.9063 (t) cc_final: 0.8803 (m)
REVERT: B  481 ILE cc_start: 0.9251 (mm) cc_final: 0.8983 (mm)
REVERT: B  959 TRP cc_start: 0.7048 (p-90) cc_final: 0.6651 (p-90)
REVERT: B  988 TYR cc_start: 0.7541 (p90) cc_final: 0.7246 (p90)
REVERT: C   47 LEU cc_start: 0.4639 (OUTLIER) cc_final: 0.4166 (tp)
REVERT: C  179 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6497 (pt)
REVERT: C  194 GLN cc_start: 0.5639 (OUTLIER) cc_final: 0.5283 (mp10)
REVERT: C  210 PHE cc_start: 0.4930 (OUTLIER) cc_final: 0.4579 (t80)
  outliers start: 66
  outliers final: 36
  residues processed: 215
  average time/residue: 0.2269
  time to fit residues: 72.5309
Evaluate side-chains
  186 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 142
  time to evaluate  : 1.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1188 THR
Chi-restraints excluded: chain A residue 1207 ILE
Chi-restraints excluded: chain A residue 1303 VAL
Chi-restraints excluded: chain A residue 1375 VAL
Chi-restraints excluded: chain A residue 1384 TRP
Chi-restraints excluded: chain A residue 1410 LEU
Chi-restraints excluded: chain A residue 1412 CYS
Chi-restraints excluded: chain A residue 1447 HIS
Chi-restraints excluded: chain A residue 1476 LYS
Chi-restraints excluded: chain A residue 1479 GLU
Chi-restraints excluded: chain A residue 1514 THR
Chi-restraints excluded: chain A residue 1529 ARG
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  412 HIS
Chi-restraints excluded: chain B residue  425 LEU
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain B residue  503 CYS
Chi-restraints excluded: chain B residue  550 THR
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  717 THR
Chi-restraints excluded: chain B residue  727 TRP
Chi-restraints excluded: chain B residue  808 VAL
Chi-restraints excluded: chain B residue  809 VAL
Chi-restraints excluded: chain B residue  833 LEU
Chi-restraints excluded: chain B residue  845 THR
Chi-restraints excluded: chain B residue  899 VAL
Chi-restraints excluded: chain B residue  910 CYS
Chi-restraints excluded: chain B residue  918 VAL
Chi-restraints excluded: chain B residue  940 LEU
Chi-restraints excluded: chain B residue 1004 PHE
Chi-restraints excluded: chain B residue 1056 VAL
Chi-restraints excluded: chain B residue 1078 HIS
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  194 GLN
Chi-restraints excluded: chain C residue  197 CYS
Chi-restraints excluded: chain C residue  205 CYS
Chi-restraints excluded: chain C residue  210 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 130 optimal weight:    0.0050
   chunk 137 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   chunk 104 optimal weight:    0.9990
   chunk 18 optimal weight:    6.9990
   chunk 66 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 116 optimal weight:    3.9990
   chunk 63 optimal weight:    0.7980
   chunk 131 optimal weight:    0.7980
   overall best weight:    0.7198

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

Flipped N/Q/H residues before XYZ refinement:
A1302 HIS
** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 232 ASN
** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 545 HIS
B 570 ASN
B 834 ASN
** C  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  82 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.170421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.146544 restraints weight = 16699.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.141155 restraints weight = 27199.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.139597 restraints weight = 31497.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13133  Z= 0.116
  Angle     :  0.527   8.088  17880  Z= 0.272
  Chirality :  0.043   0.155   1926
  Planarity :  0.004   0.039   2346
  Dihedral  :  6.705  57.904   1791
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 14.03 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.20), residues: 1620
  helix: -0.91 (0.32), residues: 248
  sheet: -0.79 (0.29), residues: 317
  loop : -0.93 (0.19), residues: 1055

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 179 
 HIS   0.005   0.001   HIS B  78 
 PHE   0.021   0.001   PHE B1010 
 TYR   0.024   0.001   TYR B 558 
 ARG   0.003   0.000   ARG A1172 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03688 (  303)
  hydrogen bonds       : angle       5.72347 (  846)
  metal coordination   : bond        0.00179 (    3)
  SS BOND              : bond        0.00292 (   42)
  SS BOND              : angle       1.01582 (   84)
  covalent geometry    : bond        0.00272 (13088)
  covalent geometry    : angle       0.52333 (17796)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 157
  time to evaluate  : 1.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1169 GLN cc_start: 0.7437 (mp10) cc_final: 0.7109 (mm-40)
REVERT: A 1384 TRP cc_start: 0.3433 (OUTLIER) cc_final: 0.3045 (m-90)
REVERT: A 1455 GLU cc_start: 0.7395 (tm-30) cc_final: 0.6823 (tm-30)
REVERT: A 1479 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.5791 (tp30)
REVERT: B  175 HIS cc_start: 0.7547 (OUTLIER) cc_final: 0.7210 (m-70)
REVERT: B  246 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7378 (mm)
REVERT: B  407 ASP cc_start: 0.7072 (m-30) cc_final: 0.6860 (m-30)
REVERT: B  412 HIS cc_start: 0.5592 (OUTLIER) cc_final: 0.5128 (p90)
REVERT: B  479 THR cc_start: 0.9114 (t) cc_final: 0.8843 (m)
REVERT: B  481 ILE cc_start: 0.9263 (mm) cc_final: 0.9029 (mm)
REVERT: B  788 MET cc_start: 0.8784 (ttm) cc_final: 0.8460 (ttp)
REVERT: B  959 TRP cc_start: 0.7050 (p-90) cc_final: 0.6389 (p-90)
REVERT: B  988 TYR cc_start: 0.7527 (p90) cc_final: 0.7263 (p90)
REVERT: B 1078 HIS cc_start: 0.6130 (OUTLIER) cc_final: 0.5009 (m-70)
REVERT: C   47 LEU cc_start: 0.4499 (OUTLIER) cc_final: 0.4033 (tp)
REVERT: C  179 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6436 (pt)
REVERT: C  194 GLN cc_start: 0.5403 (OUTLIER) cc_final: 0.5186 (mm-40)
  outliers start: 59
  outliers final: 38
  residues processed: 205
  average time/residue: 0.2339
  time to fit residues: 72.0374
Evaluate side-chains
  191 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 144
  time to evaluate  : 1.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1188 THR
Chi-restraints excluded: chain A residue 1207 ILE
Chi-restraints excluded: chain A residue 1282 CYS
Chi-restraints excluded: chain A residue 1303 VAL
Chi-restraints excluded: chain A residue 1357 GLU
Chi-restraints excluded: chain A residue 1375 VAL
Chi-restraints excluded: chain A residue 1384 TRP
Chi-restraints excluded: chain A residue 1410 LEU
Chi-restraints excluded: chain A residue 1412 CYS
Chi-restraints excluded: chain A residue 1447 HIS
Chi-restraints excluded: chain A residue 1476 LYS
Chi-restraints excluded: chain A residue 1479 GLU
Chi-restraints excluded: chain A residue 1513 VAL
Chi-restraints excluded: chain A residue 1514 THR
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  175 HIS
Chi-restraints excluded: chain B residue  232 ASN
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  412 HIS
Chi-restraints excluded: chain B residue  425 LEU
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain B residue  503 CYS
Chi-restraints excluded: chain B residue  550 THR
Chi-restraints excluded: chain B residue  568 THR
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  717 THR
Chi-restraints excluded: chain B residue  727 TRP
Chi-restraints excluded: chain B residue  808 VAL
Chi-restraints excluded: chain B residue  809 VAL
Chi-restraints excluded: chain B residue  845 THR
Chi-restraints excluded: chain B residue  899 VAL
Chi-restraints excluded: chain B residue  918 VAL
Chi-restraints excluded: chain B residue  940 LEU
Chi-restraints excluded: chain B residue 1056 VAL
Chi-restraints excluded: chain B residue 1057 LEU
Chi-restraints excluded: chain B residue 1078 HIS
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   88 PHE
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  194 GLN
Chi-restraints excluded: chain C residue  197 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 140 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 144 optimal weight:    0.7980
   chunk 149 optimal weight:    0.0980
   chunk 73 optimal weight:   10.0000
   chunk 132 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9990
   chunk 146 optimal weight:    7.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 232 ASN
B 234 HIS
B 545 HIS
** C  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  82 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.171241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.148863 restraints weight = 16574.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.145388 restraints weight = 26076.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.142886 restraints weight = 26756.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  13133  Z= 0.117
  Angle     :  0.524   7.652  17880  Z= 0.269
  Chirality :  0.043   0.198   1926
  Planarity :  0.004   0.038   2346
  Dihedral  :  6.377  57.750   1787
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 14.52 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.21), residues: 1620
  helix: -0.61 (0.33), residues: 248
  sheet: -0.96 (0.29), residues: 317
  loop : -0.81 (0.19), residues: 1055

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 179 
 HIS   0.005   0.001   HIS B  78 
 PHE   0.014   0.001   PHE B 912 
 TYR   0.012   0.001   TYR B 776 
 ARG   0.006   0.000   ARG B 292 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03420 (  303)
  hydrogen bonds       : angle       5.50315 (  846)
  metal coordination   : bond        0.00168 (    3)
  SS BOND              : bond        0.00334 (   42)
  SS BOND              : angle       1.28330 (   84)
  covalent geometry    : bond        0.00278 (13088)
  covalent geometry    : angle       0.51799 (17796)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 155
  time to evaluate  : 1.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1169 GLN cc_start: 0.7391 (mp10) cc_final: 0.7097 (mm-40)
REVERT: A 1384 TRP cc_start: 0.3343 (OUTLIER) cc_final: 0.2998 (m-90)
REVERT: A 1455 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6845 (tm-30)
REVERT: A 1479 GLU cc_start: 0.6182 (OUTLIER) cc_final: 0.5738 (tp30)
REVERT: B  175 HIS cc_start: 0.7455 (OUTLIER) cc_final: 0.7245 (m170)
REVERT: B  246 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7386 (mm)
REVERT: B  407 ASP cc_start: 0.7078 (m-30) cc_final: 0.6862 (m-30)
REVERT: B  412 HIS cc_start: 0.5569 (OUTLIER) cc_final: 0.5099 (p90)
REVERT: B  479 THR cc_start: 0.9127 (t) cc_final: 0.8836 (m)
REVERT: B  481 ILE cc_start: 0.9285 (mm) cc_final: 0.9044 (mm)
REVERT: B  959 TRP cc_start: 0.7031 (p-90) cc_final: 0.6319 (p-90)
REVERT: B  962 ILE cc_start: 0.8675 (mm) cc_final: 0.8179 (mm)
REVERT: B  988 TYR cc_start: 0.7497 (p90) cc_final: 0.7217 (p90)
REVERT: B 1078 HIS cc_start: 0.6071 (OUTLIER) cc_final: 0.4970 (m-70)
REVERT: C   47 LEU cc_start: 0.4468 (OUTLIER) cc_final: 0.3866 (tm)
REVERT: C  179 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6358 (pt)
REVERT: C  210 PHE cc_start: 0.4952 (OUTLIER) cc_final: 0.4626 (t80)
  outliers start: 70
  outliers final: 42
  residues processed: 212
  average time/residue: 0.2200
  time to fit residues: 71.1713
Evaluate side-chains
  194 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 143
  time to evaluate  : 1.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1188 THR
Chi-restraints excluded: chain A residue 1282 CYS
Chi-restraints excluded: chain A residue 1303 VAL
Chi-restraints excluded: chain A residue 1357 GLU
Chi-restraints excluded: chain A residue 1375 VAL
Chi-restraints excluded: chain A residue 1384 TRP
Chi-restraints excluded: chain A residue 1410 LEU
Chi-restraints excluded: chain A residue 1412 CYS
Chi-restraints excluded: chain A residue 1447 HIS
Chi-restraints excluded: chain A residue 1476 LYS
Chi-restraints excluded: chain A residue 1479 GLU
Chi-restraints excluded: chain A residue 1513 VAL
Chi-restraints excluded: chain A residue 1514 THR
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  175 HIS
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  293 GLU
Chi-restraints excluded: chain B residue  412 HIS
Chi-restraints excluded: chain B residue  425 LEU
Chi-restraints excluded: chain B residue  473 MET
Chi-restraints excluded: chain B residue  488 LEU
Chi-restraints excluded: chain B residue  497 ILE
Chi-restraints excluded: chain B residue  503 CYS
Chi-restraints excluded: chain B residue  550 THR
Chi-restraints excluded: chain B residue  568 THR
Chi-restraints excluded: chain B residue  587 GLN
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  715 SER
Chi-restraints excluded: chain B residue  717 THR
Chi-restraints excluded: chain B residue  727 TRP
Chi-restraints excluded: chain B residue  808 VAL
Chi-restraints excluded: chain B residue  809 VAL
Chi-restraints excluded: chain B residue  845 THR
Chi-restraints excluded: chain B residue  852 SER
Chi-restraints excluded: chain B residue  899 VAL
Chi-restraints excluded: chain B residue  918 VAL
Chi-restraints excluded: chain B residue 1056 VAL
Chi-restraints excluded: chain B residue 1057 LEU
Chi-restraints excluded: chain B residue 1078 HIS
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   88 PHE
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  161 HIS
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  197 CYS
Chi-restraints excluded: chain C residue  205 CYS
Chi-restraints excluded: chain C residue  210 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 81 optimal weight:    0.0470
   chunk 108 optimal weight:    5.9990
   chunk 115 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 107 optimal weight:    0.0040
   chunk 126 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.6090

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

Flipped N/Q/H residues before XYZ refinement:
A1236 HIS
** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 234 HIS
B 545 HIS
B 584 GLN
C  82 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.170971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.146072 restraints weight = 16741.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.141631 restraints weight = 27655.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.140078 restraints weight = 30192.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  13133  Z= 0.112
  Angle     :  0.534   8.319  17880  Z= 0.275
  Chirality :  0.043   0.261   1926
  Planarity :  0.004   0.037   2346
  Dihedral  :  6.173  57.261   1783
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 15.84 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.21), residues: 1620
  helix: -0.62 (0.33), residues: 242
  sheet: -0.87 (0.30), residues: 305
  loop : -0.77 (0.19), residues: 1073

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 179 
 HIS   0.006   0.001   HIS B 492 
 PHE   0.014   0.001   PHE B 912 
 TYR   0.016   0.001   TYR B 309 
 ARG   0.008   0.000   ARG B 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03401 (  303)
  hydrogen bonds       : angle       5.45168 (  846)
  metal coordination   : bond        0.00025 (    3)
  SS BOND              : bond        0.00368 (   42)
  SS BOND              : angle       1.68621 (   84)
  covalent geometry    : bond        0.00268 (13088)
  covalent geometry    : angle       0.52293 (17796)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 152
  time to evaluate  : 1.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1169 GLN cc_start: 0.7413 (mp10) cc_final: 0.7027 (mm-40)
REVERT: A 1384 TRP cc_start: 0.3324 (OUTLIER) cc_final: 0.2982 (m-90)
REVERT: A 1455 GLU cc_start: 0.7347 (tm-30) cc_final: 0.6865 (tm-30)
REVERT: A 1479 GLU cc_start: 0.6131 (pt0) cc_final: 0.5730 (tp30)
REVERT: B  412 HIS cc_start: 0.5439 (OUTLIER) cc_final: 0.4968 (p90)
REVERT: B  473 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6798 (ttt)
REVERT: B  479 THR cc_start: 0.9089 (t) cc_final: 0.8782 (m)
REVERT: B  481 ILE cc_start: 0.9282 (mm) cc_final: 0.9018 (mm)
REVERT: B  959 TRP cc_start: 0.7008 (p-90) cc_final: 0.6263 (p-90)
REVERT: B  962 ILE cc_start: 0.8650 (mm) cc_final: 0.8302 (mm)
REVERT: B  988 TYR cc_start: 0.7481 (p90) cc_final: 0.7180 (p90)
REVERT: B 1078 HIS cc_start: 0.6048 (OUTLIER) cc_final: 0.4972 (m-70)
REVERT: C   47 LEU cc_start: 0.4407 (OUTLIER) cc_final: 0.3883 (tm)
REVERT: C  179 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6265 (pt)
REVERT: C  194 GLN cc_start: 0.5403 (OUTLIER) cc_final: 0.5139 (mm-40)
REVERT: C  210 PHE cc_start: 0.5338 (OUTLIER) cc_final: 0.4868 (t80)
  outliers start: 58
  outliers final: 37
  residues processed: 199
  average time/residue: 0.2149
  time to fit residues: 64.8548
Evaluate side-chains
  189 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 144
  time to evaluate  : 1.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1188 THR
Chi-restraints excluded: chain A residue 1207 ILE
Chi-restraints excluded: chain A residue 1282 CYS
Chi-restraints excluded: chain A residue 1303 VAL
Chi-restraints excluded: chain A residue 1357 GLU
Chi-restraints excluded: chain A residue 1375 VAL
Chi-restraints excluded: chain A residue 1384 TRP
Chi-restraints excluded: chain A residue 1412 CYS
Chi-restraints excluded: chain A residue 1447 HIS
Chi-restraints excluded: chain A residue 1476 LYS
Chi-restraints excluded: chain A residue 1513 VAL
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  293 GLU
Chi-restraints excluded: chain B residue  412 HIS
Chi-restraints excluded: chain B residue  425 LEU
Chi-restraints excluded: chain B residue  473 MET
Chi-restraints excluded: chain B residue  497 ILE
Chi-restraints excluded: chain B residue  550 THR
Chi-restraints excluded: chain B residue  587 GLN
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  715 SER
Chi-restraints excluded: chain B residue  717 THR
Chi-restraints excluded: chain B residue  727 TRP
Chi-restraints excluded: chain B residue  808 VAL
Chi-restraints excluded: chain B residue  845 THR
Chi-restraints excluded: chain B residue  852 SER
Chi-restraints excluded: chain B residue  899 VAL
Chi-restraints excluded: chain B residue  940 LEU
Chi-restraints excluded: chain B residue 1056 VAL
Chi-restraints excluded: chain B residue 1057 LEU
Chi-restraints excluded: chain B residue 1078 HIS
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   88 PHE
Chi-restraints excluded: chain C residue  161 HIS
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  194 GLN
Chi-restraints excluded: chain C residue  197 CYS
Chi-restraints excluded: chain C residue  205 CYS
Chi-restraints excluded: chain C residue  210 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 145 optimal weight:    5.9990
   chunk 118 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 122 optimal weight:    3.9990
   chunk 139 optimal weight:    8.9990
   chunk 73 optimal weight:   10.0000
   chunk 81 optimal weight:    2.9990
   chunk 157 optimal weight:    6.9990
   chunk 99 optimal weight:    2.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 752 ASN
C  82 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.167043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.142870 restraints weight = 16969.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.138635 restraints weight = 27717.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.136248 restraints weight = 32166.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.2019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074  13133  Z= 0.209
  Angle     :  0.601  12.383  17880  Z= 0.313
  Chirality :  0.045   0.273   1926
  Planarity :  0.004   0.039   2346
  Dihedral  :  6.118  58.982   1770
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 16.19 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.21), residues: 1620
  helix: -0.64 (0.34), residues: 242
  sheet: -0.92 (0.30), residues: 302
  loop : -0.89 (0.19), residues: 1076

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 842 
 HIS   0.008   0.001   HIS B 492 
 PHE   0.022   0.002   PHE B 912 
 TYR   0.015   0.002   TYR B 776 
 ARG   0.008   0.000   ARG B 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03716 (  303)
  hydrogen bonds       : angle       5.58015 (  846)
  metal coordination   : bond        0.00375 (    3)
  SS BOND              : bond        0.00497 (   42)
  SS BOND              : angle       1.56337 (   84)
  covalent geometry    : bond        0.00500 (13088)
  covalent geometry    : angle       0.59271 (17796)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 155
  time to evaluate  : 1.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1384 TRP cc_start: 0.3547 (OUTLIER) cc_final: 0.3139 (m-90)
REVERT: B  412 HIS cc_start: 0.5840 (OUTLIER) cc_final: 0.5364 (p90)
REVERT: B  481 ILE cc_start: 0.9281 (mm) cc_final: 0.9042 (mm)
REVERT: B 1078 HIS cc_start: 0.6115 (OUTLIER) cc_final: 0.4955 (m-70)
REVERT: C   47 LEU cc_start: 0.4574 (OUTLIER) cc_final: 0.3964 (tm)
REVERT: C  179 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6352 (pt)
REVERT: C  210 PHE cc_start: 0.5087 (OUTLIER) cc_final: 0.4745 (t80)
  outliers start: 63
  outliers final: 44
  residues processed: 206
  average time/residue: 0.2060
  time to fit residues: 64.5334
Evaluate side-chains
  193 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 143
  time to evaluate  : 1.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1188 THR
Chi-restraints excluded: chain A residue 1207 ILE
Chi-restraints excluded: chain A residue 1282 CYS
Chi-restraints excluded: chain A residue 1303 VAL
Chi-restraints excluded: chain A residue 1357 GLU
Chi-restraints excluded: chain A residue 1375 VAL
Chi-restraints excluded: chain A residue 1384 TRP
Chi-restraints excluded: chain A residue 1410 LEU
Chi-restraints excluded: chain A residue 1412 CYS
Chi-restraints excluded: chain A residue 1447 HIS
Chi-restraints excluded: chain A residue 1476 LYS
Chi-restraints excluded: chain A residue 1513 VAL
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  293 GLU
Chi-restraints excluded: chain B residue  380 ASP
Chi-restraints excluded: chain B residue  412 HIS
Chi-restraints excluded: chain B residue  415 TYR
Chi-restraints excluded: chain B residue  425 LEU
Chi-restraints excluded: chain B residue  473 MET
Chi-restraints excluded: chain B residue  497 ILE
Chi-restraints excluded: chain B residue  550 THR
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  715 SER
Chi-restraints excluded: chain B residue  717 THR
Chi-restraints excluded: chain B residue  808 VAL
Chi-restraints excluded: chain B residue  845 THR
Chi-restraints excluded: chain B residue  852 SER
Chi-restraints excluded: chain B residue  899 VAL
Chi-restraints excluded: chain B residue  918 VAL
Chi-restraints excluded: chain B residue  940 LEU
Chi-restraints excluded: chain B residue 1038 ILE
Chi-restraints excluded: chain B residue 1056 VAL
Chi-restraints excluded: chain B residue 1057 LEU
Chi-restraints excluded: chain B residue 1078 HIS
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain C residue  135 LEU
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  161 HIS
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  197 CYS
Chi-restraints excluded: chain C residue  205 CYS
Chi-restraints excluded: chain C residue  210 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 91 optimal weight:    0.6980
   chunk 93 optimal weight:    0.1980
   chunk 154 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 144 optimal weight:    3.9990
   chunk 129 optimal weight:    2.9990
   chunk 157 optimal weight:    6.9990
   chunk 21 optimal weight:    8.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  83 GLN
** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 285 HIS
** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.169859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.146107 restraints weight = 16622.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.141672 restraints weight = 26224.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.139679 restraints weight = 25499.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078  13133  Z= 0.120
  Angle     :  0.559  13.859  17880  Z= 0.291
  Chirality :  0.043   0.248   1926
  Planarity :  0.004   0.037   2346
  Dihedral  :  5.857  56.808   1768
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 17.24 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.03 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.21), residues: 1620
  helix: -0.48 (0.34), residues: 236
  sheet: -0.99 (0.29), residues: 316
  loop : -0.79 (0.20), residues: 1068

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 959 
 HIS   0.005   0.001   HIS B 492 
 PHE   0.012   0.001   PHE B 912 
 TYR   0.014   0.001   TYR B 776 
 ARG   0.007   0.000   ARG B 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03310 (  303)
  hydrogen bonds       : angle       5.39041 (  846)
  metal coordination   : bond        0.00142 (    3)
  SS BOND              : bond        0.00429 (   42)
  SS BOND              : angle       1.53086 (   84)
  covalent geometry    : bond        0.00291 (13088)
  covalent geometry    : angle       0.55047 (17796)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 147
  time to evaluate  : 1.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1384 TRP cc_start: 0.3439 (OUTLIER) cc_final: 0.3074 (m-90)
REVERT: B  175 HIS cc_start: 0.7293 (m-70) cc_final: 0.6933 (m-70)
REVERT: B  412 HIS cc_start: 0.5625 (OUTLIER) cc_final: 0.5160 (p90)
REVERT: B  473 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6780 (ttt)
REVERT: B  788 MET cc_start: 0.8582 (ttm) cc_final: 0.8261 (ttp)
REVERT: B  959 TRP cc_start: 0.6987 (p-90) cc_final: 0.6676 (p-90)
REVERT: B 1078 HIS cc_start: 0.6134 (OUTLIER) cc_final: 0.5062 (m-70)
REVERT: C   47 LEU cc_start: 0.4624 (OUTLIER) cc_final: 0.4092 (tm)
REVERT: C  109 CYS cc_start: 0.4318 (t) cc_final: 0.4054 (t)
REVERT: C  179 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6266 (pt)
REVERT: C  194 GLN cc_start: 0.5362 (OUTLIER) cc_final: 0.5072 (mm-40)
REVERT: C  210 PHE cc_start: 0.5363 (OUTLIER) cc_final: 0.4897 (t80)
  outliers start: 55
  outliers final: 40
  residues processed: 193
  average time/residue: 0.2158
  time to fit residues: 63.4948
Evaluate side-chains
  190 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 142
  time to evaluate  : 1.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1188 THR
Chi-restraints excluded: chain A residue 1207 ILE
Chi-restraints excluded: chain A residue 1282 CYS
Chi-restraints excluded: chain A residue 1303 VAL
Chi-restraints excluded: chain A residue 1357 GLU
Chi-restraints excluded: chain A residue 1375 VAL
Chi-restraints excluded: chain A residue 1384 TRP
Chi-restraints excluded: chain A residue 1412 CYS
Chi-restraints excluded: chain A residue 1447 HIS
Chi-restraints excluded: chain A residue 1476 LYS
Chi-restraints excluded: chain A residue 1513 VAL
Chi-restraints excluded: chain A residue 1514 THR
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  293 GLU
Chi-restraints excluded: chain B residue  380 ASP
Chi-restraints excluded: chain B residue  412 HIS
Chi-restraints excluded: chain B residue  425 LEU
Chi-restraints excluded: chain B residue  473 MET
Chi-restraints excluded: chain B residue  497 ILE
Chi-restraints excluded: chain B residue  550 THR
Chi-restraints excluded: chain B residue  587 GLN
Chi-restraints excluded: chain B residue  701 CYS
Chi-restraints excluded: chain B residue  703 LEU
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  715 SER
Chi-restraints excluded: chain B residue  717 THR
Chi-restraints excluded: chain B residue  808 VAL
Chi-restraints excluded: chain B residue  845 THR
Chi-restraints excluded: chain B residue  852 SER
Chi-restraints excluded: chain B residue  899 VAL
Chi-restraints excluded: chain B residue  940 LEU
Chi-restraints excluded: chain B residue 1056 VAL
Chi-restraints excluded: chain B residue 1057 LEU
Chi-restraints excluded: chain B residue 1078 HIS
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   88 PHE
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  194 GLN
Chi-restraints excluded: chain C residue  197 CYS
Chi-restraints excluded: chain C residue  205 CYS
Chi-restraints excluded: chain C residue  210 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 135 optimal weight:    8.9990
   chunk 149 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 88 optimal weight:    0.0570
   chunk 49 optimal weight:    2.9990
   chunk 137 optimal weight:    7.9990
   chunk 99 optimal weight:    2.9990
   chunk 117 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 59 optimal weight:    1.9990
   chunk 109 optimal weight:    3.9990
   overall best weight:    2.4106

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

Flipped N/Q/H residues before XYZ refinement:
** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 153 GLN
B 234 HIS
B 350 HIS
** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1078 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.164495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.140941 restraints weight = 17004.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.136391 restraints weight = 27596.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.133998 restraints weight = 28496.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068  13133  Z= 0.276
  Angle     :  0.671  14.415  17880  Z= 0.351
  Chirality :  0.047   0.235   1926
  Planarity :  0.004   0.039   2346
  Dihedral  :  6.428  59.777   1768
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 17.10 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.21), residues: 1620
  helix: -0.82 (0.33), residues: 242
  sheet: -1.11 (0.30), residues: 302
  loop : -1.05 (0.19), residues: 1076

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 959 
 HIS   0.007   0.001   HIS B 492 
 PHE   0.025   0.002   PHE B 912 
 TYR   0.019   0.002   TYR B 776 
 ARG   0.008   0.001   ARG B 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03890 (  303)
  hydrogen bonds       : angle       5.85014 (  846)
  metal coordination   : bond        0.00536 (    3)
  SS BOND              : bond        0.00565 (   42)
  SS BOND              : angle       1.87155 (   84)
  covalent geometry    : bond        0.00662 (13088)
  covalent geometry    : angle       0.65987 (17796)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 147
  time to evaluate  : 1.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1193 LYS cc_start: 0.7128 (mmtm) cc_final: 0.6810 (mmtp)
REVERT: A 1384 TRP cc_start: 0.3523 (OUTLIER) cc_final: 0.2985 (m-90)
REVERT: B  285 HIS cc_start: 0.5866 (t70) cc_final: 0.5206 (t-90)
REVERT: B  293 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7513 (pp20)
REVERT: B  412 HIS cc_start: 0.5905 (OUTLIER) cc_final: 0.5384 (p90)
REVERT: B  831 MET cc_start: 0.8146 (mpp) cc_final: 0.7517 (mpp)
REVERT: B  959 TRP cc_start: 0.7151 (p-90) cc_final: 0.6833 (p-90)
REVERT: C  109 CYS cc_start: 0.4532 (t) cc_final: 0.4259 (t)
REVERT: C  179 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6406 (pt)
REVERT: C  210 PHE cc_start: 0.5153 (OUTLIER) cc_final: 0.4790 (t80)
  outliers start: 63
  outliers final: 51
  residues processed: 200
  average time/residue: 0.2168
  time to fit residues: 66.4194
Evaluate side-chains
  198 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 142
  time to evaluate  : 1.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1188 THR
Chi-restraints excluded: chain A residue 1207 ILE
Chi-restraints excluded: chain A residue 1274 ASN
Chi-restraints excluded: chain A residue 1282 CYS
Chi-restraints excluded: chain A residue 1303 VAL
Chi-restraints excluded: chain A residue 1307 SER
Chi-restraints excluded: chain A residue 1357 GLU
Chi-restraints excluded: chain A residue 1375 VAL
Chi-restraints excluded: chain A residue 1384 TRP
Chi-restraints excluded: chain A residue 1412 CYS
Chi-restraints excluded: chain A residue 1447 HIS
Chi-restraints excluded: chain A residue 1476 LYS
Chi-restraints excluded: chain A residue 1513 VAL
Chi-restraints excluded: chain A residue 1514 THR
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  293 GLU
Chi-restraints excluded: chain B residue  380 ASP
Chi-restraints excluded: chain B residue  412 HIS
Chi-restraints excluded: chain B residue  425 LEU
Chi-restraints excluded: chain B residue  473 MET
Chi-restraints excluded: chain B residue  497 ILE
Chi-restraints excluded: chain B residue  550 THR
Chi-restraints excluded: chain B residue  568 THR
Chi-restraints excluded: chain B residue  587 GLN
Chi-restraints excluded: chain B residue  674 LYS
Chi-restraints excluded: chain B residue  701 CYS
Chi-restraints excluded: chain B residue  703 LEU
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  715 SER
Chi-restraints excluded: chain B residue  717 THR
Chi-restraints excluded: chain B residue  808 VAL
Chi-restraints excluded: chain B residue  816 MET
Chi-restraints excluded: chain B residue  845 THR
Chi-restraints excluded: chain B residue  852 SER
Chi-restraints excluded: chain B residue  899 VAL
Chi-restraints excluded: chain B residue  918 VAL
Chi-restraints excluded: chain B residue  940 LEU
Chi-restraints excluded: chain B residue 1038 ILE
Chi-restraints excluded: chain B residue 1056 VAL
Chi-restraints excluded: chain B residue 1057 LEU
Chi-restraints excluded: chain B residue 1065 ILE
Chi-restraints excluded: chain B residue 1078 HIS
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain C residue  135 LEU
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  197 CYS
Chi-restraints excluded: chain C residue  205 CYS
Chi-restraints excluded: chain C residue  210 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 162 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 122 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 112 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9980
   chunk 5 optimal weight:    7.9990
   chunk 74 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 11 optimal weight:    2.9990
   chunk 87 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 234 HIS
** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 134 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.168989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.147680 restraints weight = 16632.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.143050 restraints weight = 25022.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.142160 restraints weight = 25748.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  13133  Z= 0.126
  Angle     :  0.568  12.905  17880  Z= 0.296
  Chirality :  0.044   0.222   1926
  Planarity :  0.004   0.037   2346
  Dihedral  :  5.988  57.555   1766
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 17.79 %
    Favored  : 78.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.21), residues: 1620
  helix: -0.59 (0.34), residues: 241
  sheet: -1.08 (0.30), residues: 316
  loop : -0.83 (0.20), residues: 1063

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 764 
 HIS   0.010   0.001   HIS B 175 
 PHE   0.012   0.001   PHE B 306 
 TYR   0.015   0.001   TYR B 776 
 ARG   0.007   0.000   ARG B 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03358 (  303)
  hydrogen bonds       : angle       5.48630 (  846)
  metal coordination   : bond        0.00155 (    3)
  SS BOND              : bond        0.00414 (   42)
  SS BOND              : angle       1.49629 (   84)
  covalent geometry    : bond        0.00302 (13088)
  covalent geometry    : angle       0.55971 (17796)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 148
  time to evaluate  : 1.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1384 TRP cc_start: 0.3557 (OUTLIER) cc_final: 0.3133 (m-90)
REVERT: B  285 HIS cc_start: 0.5523 (t70) cc_final: 0.5047 (t-90)
REVERT: B  309 TYR cc_start: 0.9001 (m-10) cc_final: 0.8592 (m-10)
REVERT: B  412 HIS cc_start: 0.5529 (OUTLIER) cc_final: 0.5112 (p90)
REVERT: B  959 TRP cc_start: 0.6965 (p-90) cc_final: 0.6764 (p-90)
REVERT: B 1078 HIS cc_start: 0.6166 (OUTLIER) cc_final: 0.4948 (m-70)
REVERT: C  179 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6262 (pt)
REVERT: C  194 GLN cc_start: 0.5564 (OUTLIER) cc_final: 0.5041 (mm-40)
REVERT: C  210 PHE cc_start: 0.5359 (OUTLIER) cc_final: 0.4856 (t80)
  outliers start: 54
  outliers final: 46
  residues processed: 194
  average time/residue: 0.2189
  time to fit residues: 65.3061
Evaluate side-chains
  193 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 141
  time to evaluate  : 1.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1168 LEU
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1188 THR
Chi-restraints excluded: chain A residue 1207 ILE
Chi-restraints excluded: chain A residue 1282 CYS
Chi-restraints excluded: chain A residue 1303 VAL
Chi-restraints excluded: chain A residue 1307 SER
Chi-restraints excluded: chain A residue 1357 GLU
Chi-restraints excluded: chain A residue 1375 VAL
Chi-restraints excluded: chain A residue 1384 TRP
Chi-restraints excluded: chain A residue 1410 LEU
Chi-restraints excluded: chain A residue 1412 CYS
Chi-restraints excluded: chain A residue 1447 HIS
Chi-restraints excluded: chain A residue 1476 LYS
Chi-restraints excluded: chain A residue 1513 VAL
Chi-restraints excluded: chain A residue 1514 THR
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue   31 ASP
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  293 GLU
Chi-restraints excluded: chain B residue  380 ASP
Chi-restraints excluded: chain B residue  412 HIS
Chi-restraints excluded: chain B residue  473 MET
Chi-restraints excluded: chain B residue  497 ILE
Chi-restraints excluded: chain B residue  550 THR
Chi-restraints excluded: chain B residue  587 GLN
Chi-restraints excluded: chain B residue  701 CYS
Chi-restraints excluded: chain B residue  703 LEU
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  715 SER
Chi-restraints excluded: chain B residue  717 THR
Chi-restraints excluded: chain B residue  808 VAL
Chi-restraints excluded: chain B residue  845 THR
Chi-restraints excluded: chain B residue  852 SER
Chi-restraints excluded: chain B residue  899 VAL
Chi-restraints excluded: chain B residue  918 VAL
Chi-restraints excluded: chain B residue  940 LEU
Chi-restraints excluded: chain B residue 1056 VAL
Chi-restraints excluded: chain B residue 1057 LEU
Chi-restraints excluded: chain B residue 1078 HIS
Chi-restraints excluded: chain C residue   88 PHE
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  194 GLN
Chi-restraints excluded: chain C residue  197 CYS
Chi-restraints excluded: chain C residue  205 CYS
Chi-restraints excluded: chain C residue  210 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 105 optimal weight:    1.9990
   chunk 124 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 9 optimal weight:    7.9990
   chunk 106 optimal weight:    2.9990
   chunk 140 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 82 optimal weight:    0.0270
   chunk 149 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0470
   overall best weight:    1.4142

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

Flipped N/Q/H residues before XYZ refinement:
** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 234 HIS
** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.167038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.142951 restraints weight = 16739.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.137704 restraints weight = 25645.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.135798 restraints weight = 29417.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  13133  Z= 0.176
  Angle     :  0.596  12.920  17880  Z= 0.311
  Chirality :  0.045   0.218   1926
  Planarity :  0.004   0.037   2346
  Dihedral  :  6.070  58.164   1766
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 17.73 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.21), residues: 1620
  helix: -0.61 (0.34), residues: 241
  sheet: -1.09 (0.30), residues: 311
  loop : -0.86 (0.20), residues: 1068

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 842 
 HIS   0.011   0.001   HIS B 175 
 PHE   0.018   0.002   PHE B 912 
 TYR   0.017   0.001   TYR B 776 
 ARG   0.006   0.000   ARG B 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03506 (  303)
  hydrogen bonds       : angle       5.53614 (  846)
  metal coordination   : bond        0.00314 (    3)
  SS BOND              : bond        0.00447 (   42)
  SS BOND              : angle       1.60915 (   84)
  covalent geometry    : bond        0.00424 (13088)
  covalent geometry    : angle       0.58673 (17796)

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

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

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3240 Ramachandran restraints generated.
    1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 143
  time to evaluate  : 1.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1384 TRP cc_start: 0.3640 (OUTLIER) cc_final: 0.3143 (m-90)
REVERT: B  285 HIS cc_start: 0.5734 (t70) cc_final: 0.5181 (t-90)
REVERT: B  309 TYR cc_start: 0.9023 (m-10) cc_final: 0.8570 (m-10)
REVERT: B  412 HIS cc_start: 0.5761 (OUTLIER) cc_final: 0.5311 (p90)
REVERT: B  959 TRP cc_start: 0.7074 (p-90) cc_final: 0.6843 (p-90)
REVERT: B  962 ILE cc_start: 0.8538 (mm) cc_final: 0.8225 (mm)
REVERT: B 1078 HIS cc_start: 0.6126 (OUTLIER) cc_final: 0.4938 (m-70)
REVERT: C  179 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6309 (pt)
REVERT: C  210 PHE cc_start: 0.5085 (OUTLIER) cc_final: 0.4719 (t80)
  outliers start: 59
  outliers final: 51
  residues processed: 196
  average time/residue: 0.2319
  time to fit residues: 69.0682
Evaluate side-chains
  198 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 142
  time to evaluate  : 1.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1168 LEU
Chi-restraints excluded: chain A residue 1187 VAL
Chi-restraints excluded: chain A residue 1188 THR
Chi-restraints excluded: chain A residue 1207 ILE
Chi-restraints excluded: chain A residue 1274 ASN
Chi-restraints excluded: chain A residue 1282 CYS
Chi-restraints excluded: chain A residue 1303 VAL
Chi-restraints excluded: chain A residue 1307 SER
Chi-restraints excluded: chain A residue 1357 GLU
Chi-restraints excluded: chain A residue 1375 VAL
Chi-restraints excluded: chain A residue 1384 TRP
Chi-restraints excluded: chain A residue 1410 LEU
Chi-restraints excluded: chain A residue 1412 CYS
Chi-restraints excluded: chain A residue 1447 HIS
Chi-restraints excluded: chain A residue 1476 LYS
Chi-restraints excluded: chain A residue 1513 VAL
Chi-restraints excluded: chain A residue 1514 THR
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue   31 ASP
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  192 MET
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  293 GLU
Chi-restraints excluded: chain B residue  380 ASP
Chi-restraints excluded: chain B residue  412 HIS
Chi-restraints excluded: chain B residue  473 MET
Chi-restraints excluded: chain B residue  497 ILE
Chi-restraints excluded: chain B residue  550 THR
Chi-restraints excluded: chain B residue  587 GLN
Chi-restraints excluded: chain B residue  701 CYS
Chi-restraints excluded: chain B residue  703 LEU
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  715 SER
Chi-restraints excluded: chain B residue  717 THR
Chi-restraints excluded: chain B residue  808 VAL
Chi-restraints excluded: chain B residue  809 VAL
Chi-restraints excluded: chain B residue  845 THR
Chi-restraints excluded: chain B residue  852 SER
Chi-restraints excluded: chain B residue  899 VAL
Chi-restraints excluded: chain B residue  918 VAL
Chi-restraints excluded: chain B residue  940 LEU
Chi-restraints excluded: chain B residue 1056 VAL
Chi-restraints excluded: chain B residue 1057 LEU
Chi-restraints excluded: chain B residue 1065 ILE
Chi-restraints excluded: chain B residue 1078 HIS
Chi-restraints excluded: chain C residue   88 PHE
Chi-restraints excluded: chain C residue  135 LEU
Chi-restraints excluded: chain C residue  137 ARG
Chi-restraints excluded: chain C residue  167 LEU
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  197 CYS
Chi-restraints excluded: chain C residue  205 CYS
Chi-restraints excluded: chain C residue  210 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 73 optimal weight:    0.0000
   chunk 125 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 108 optimal weight:    1.9990
   chunk 107 optimal weight:    0.8980
   chunk 94 optimal weight:    0.3980
   chunk 30 optimal weight:    8.9990
   chunk 142 optimal weight:    4.9990
   chunk 141 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 234 HIS
** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.168616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.144234 restraints weight = 16544.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.140497 restraints weight = 26531.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.139782 restraints weight = 26469.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  13133  Z= 0.131
  Angle     :  0.562  12.297  17880  Z= 0.293
  Chirality :  0.044   0.210   1926
  Planarity :  0.004   0.037   2346
  Dihedral  :  5.885  57.109   1766
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 17.86 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.21), residues: 1620
  helix: -0.51 (0.34), residues: 242
  sheet: -1.01 (0.29), residues: 310
  loop : -0.76 (0.20), residues: 1068

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 727 
 HIS   0.008   0.001   HIS B 175 
 PHE   0.013   0.001   PHE B 912 
 TYR   0.016   0.001   TYR B 776 
 ARG   0.006   0.000   ARG B 109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03252 (  303)
  hydrogen bonds       : angle       5.42372 (  846)
  metal coordination   : bond        0.00157 (    3)
  SS BOND              : bond        0.00395 (   42)
  SS BOND              : angle       1.33701 (   84)
  covalent geometry    : bond        0.00316 (13088)
  covalent geometry    : angle       0.55575 (17796)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3839.28 seconds
wall clock time: 68 minutes 12.45 seconds (4092.45 seconds total)