Starting phenix.real_space_refine
on Wed Jul 30 20:43:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y5q_33622/07_2025/7y5q_33622_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y5q_33622/07_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_33622/07_2025/7y5q_33622.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y5q_33622/07_2025/7y5q_33622.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y5q_33622/07_2025/7y5q_33622_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y5q_33622/07_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.18, per 1000 atoms: 0.56
  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: 3.76
  Conformation dependent library (CDL) restraints added in 1.5 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: 1.58
  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: 4.94

  Time building geometry restraints manager: 3.99 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:             0.940
  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:          0.460
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     34.180
  Find NCS groups from input model:        0.160
  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:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.840
-------------------------------------------------------------------------------
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  : 1.440 
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: 0.2386
  time to fit residues: 95.6364
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  : 1.536 
-------------------------------------------------------------------------------
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 = 0.3880 r_free = 0.3880 target = 0.168782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.144550 restraints weight = 16699.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.140700 restraints weight = 26871.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.139290 restraints weight = 26533.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.1229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13133  Z= 0.162
  Angle     :  0.578   7.374  17880  Z= 0.305
  Chirality :  0.044   0.175   1926
  Planarity :  0.005   0.043   2346
  Dihedral  :  7.763  59.727   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        0.04696 (  303)
  hydrogen bonds       : angle       6.31133 (  846)
  metal coordination   : bond        0.00272 (    3)
  SS BOND              : bond        0.00336 (   42)
  SS BOND              : angle       1.30827 (   84)
  covalent geometry    : bond        0.00377 (13088)
  covalent geometry    : angle       0.57201 (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  : 1.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1169 GLN cc_start: 0.7528 (mp10) cc_final: 0.7060 (mm-40)
REVERT: A 1384 TRP cc_start: 0.3477 (OUTLIER) cc_final: 0.3089 (m-90)
REVERT: A 1479 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.5895 (tp30)
REVERT: B  112 LEU cc_start: 0.8380 (mm) cc_final: 0.8161 (mm)
REVERT: B  246 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7423 (mm)
REVERT: B  407 ASP cc_start: 0.7009 (m-30) cc_final: 0.6638 (m-30)
REVERT: B  412 HIS cc_start: 0.5562 (OUTLIER) cc_final: 0.5110 (p90)
REVERT: B  479 THR cc_start: 0.9065 (t) cc_final: 0.8802 (m)
REVERT: B  481 ILE cc_start: 0.9252 (mm) cc_final: 0.8991 (mm)
REVERT: B  959 TRP cc_start: 0.7047 (p-90) cc_final: 0.6654 (p-90)
REVERT: B  988 TYR cc_start: 0.7539 (p90) cc_final: 0.7245 (p90)
REVERT: C   47 LEU cc_start: 0.4635 (OUTLIER) cc_final: 0.4182 (tp)
REVERT: C  179 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6496 (pt)
REVERT: C  194 GLN cc_start: 0.5638 (OUTLIER) cc_final: 0.5283 (mp10)
REVERT: C  210 PHE cc_start: 0.4934 (OUTLIER) cc_final: 0.4583 (t80)
  outliers start: 66
  outliers final: 36
  residues processed: 215
  average time/residue: 0.2756
  time to fit residues: 87.8769
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  : 1.751 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 137 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 79 optimal weight:   10.0000
   chunk 104 optimal weight:    0.7980
   chunk 18 optimal weight:    7.9990
   chunk 66 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 116 optimal weight:    3.9990
   chunk 63 optimal weight:    0.3980
   chunk 131 optimal weight:    0.1980
   overall best weight:    1.8784

-------------------------------------------------------------------------------
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 143 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 752 ASN
B 834 ASN
** B1078 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  82 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.165846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.140413 restraints weight = 16841.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.136049 restraints weight = 27528.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.133572 restraints weight = 29843.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  13133  Z= 0.216
  Angle     :  0.601   8.440  17880  Z= 0.313
  Chirality :  0.045   0.171   1926
  Planarity :  0.005   0.041   2346
  Dihedral  :  7.113  59.671   1791
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 14.10 %
    Favored  : 81.23 %
  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: -1.61 (0.20), residues: 1620
  helix: -1.12 (0.31), residues: 248
  sheet: -1.02 (0.29), residues: 318
  loop : -1.07 (0.19), residues: 1054

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 179 
 HIS   0.005   0.001   HIS B 492 
 PHE   0.023   0.002   PHE B  91 
 TYR   0.023   0.002   TYR B 558 
 ARG   0.003   0.000   ARG B 972 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04208 (  303)
  hydrogen bonds       : angle       5.99640 (  846)
  metal coordination   : bond        0.00429 (    3)
  SS BOND              : bond        0.00406 (   42)
  SS BOND              : angle       1.22270 (   84)
  covalent geometry    : bond        0.00510 (13088)
  covalent geometry    : angle       0.59638 (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: 67
    poor density    : 149
  time to evaluate  : 1.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1169 GLN cc_start: 0.7481 (mp10) cc_final: 0.7000 (mm-40)
REVERT: A 1384 TRP cc_start: 0.3548 (OUTLIER) cc_final: 0.3057 (m-90)
REVERT: A 1455 GLU cc_start: 0.7398 (tm-30) cc_final: 0.6750 (tm-30)
REVERT: A 1479 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.5877 (tp30)
REVERT: B  112 LEU cc_start: 0.8432 (mm) cc_final: 0.8027 (mt)
REVERT: B  174 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8093 (tm-30)
REVERT: B  293 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7493 (pp20)
REVERT: B  407 ASP cc_start: 0.7097 (m-30) cc_final: 0.6812 (m-30)
REVERT: B  412 HIS cc_start: 0.5795 (OUTLIER) cc_final: 0.5301 (p90)
REVERT: B  479 THR cc_start: 0.9177 (t) cc_final: 0.8910 (m)
REVERT: B  481 ILE cc_start: 0.9285 (mm) cc_final: 0.9029 (mm)
REVERT: B  959 TRP cc_start: 0.7119 (p-90) cc_final: 0.6370 (p-90)
REVERT: B 1098 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8832 (tt)
REVERT: C   47 LEU cc_start: 0.4662 (OUTLIER) cc_final: 0.4215 (tp)
REVERT: C  179 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6517 (pt)
REVERT: C  194 GLN cc_start: 0.5696 (OUTLIER) cc_final: 0.5429 (mp10)
REVERT: C  210 PHE cc_start: 0.5119 (OUTLIER) cc_final: 0.4763 (t80)
  outliers start: 67
  outliers final: 44
  residues processed: 203
  average time/residue: 0.2357
  time to fit residues: 72.4026
Evaluate side-chains
  197 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 143
  time to evaluate  : 1.545 
-------------------------------------------------------------------------------
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 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 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 A residue 1529 ARG
Chi-restraints excluded: chain B residue   14 SER
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  139 THR
Chi-restraints excluded: chain B residue  174 GLU
Chi-restraints excluded: chain B residue  175 HIS
Chi-restraints excluded: chain B residue  232 ASN
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  711 LEU
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  833 LEU
Chi-restraints excluded: chain B residue  845 THR
Chi-restraints excluded: chain B residue  852 SER
Chi-restraints excluded: chain B residue  858 VAL
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 1056 VAL
Chi-restraints excluded: chain B residue 1057 LEU
Chi-restraints excluded: chain B residue 1078 HIS
Chi-restraints excluded: chain B residue 1098 LEU
Chi-restraints excluded: chain C residue   47 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  179 LEU
Chi-restraints excluded: chain C residue  194 GLN
Chi-restraints excluded: chain C residue  197 CYS
Chi-restraints excluded: chain C residue  210 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 140 optimal weight:    7.9990
   chunk 36 optimal weight:    1.9990
   chunk 144 optimal weight:    0.6980
   chunk 149 optimal weight:    4.9990
   chunk 73 optimal weight:    9.9990
   chunk 132 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 23 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 72 optimal weight:    0.1980
   chunk 146 optimal weight:    7.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 143 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 285 HIS
** C  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.167520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.142809 restraints weight = 16635.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.138927 restraints weight = 29422.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.138120 restraints weight = 30104.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13133  Z= 0.149
  Angle     :  0.552   7.532  17880  Z= 0.286
  Chirality :  0.044   0.154   1926
  Planarity :  0.004   0.040   2346
  Dihedral  :  6.566  57.980   1784
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 15.56 %
    Favored  : 79.62 %
  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: -1.46 (0.21), residues: 1620
  helix: -0.90 (0.32), residues: 248
  sheet: -0.96 (0.29), residues: 313
  loop : -0.98 (0.19), residues: 1059

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 179 
 HIS   0.005   0.001   HIS B  78 
 PHE   0.016   0.001   PHE B 912 
 TYR   0.014   0.001   TYR B 776 
 ARG   0.002   0.000   ARG A1456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03708 (  303)
  hydrogen bonds       : angle       5.73480 (  846)
  metal coordination   : bond        0.00228 (    3)
  SS BOND              : bond        0.00335 (   42)
  SS BOND              : angle       1.35148 (   84)
  covalent geometry    : bond        0.00352 (13088)
  covalent geometry    : angle       0.54515 (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
  220 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 151
  time to evaluate  : 1.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1169 GLN cc_start: 0.7387 (mp10) cc_final: 0.6943 (mm-40)
REVERT: A 1384 TRP cc_start: 0.3542 (OUTLIER) cc_final: 0.3079 (m-90)
REVERT: A 1455 GLU cc_start: 0.7463 (tm-30) cc_final: 0.6917 (tm-30)
REVERT: B  112 LEU cc_start: 0.8253 (mm) cc_final: 0.8015 (mm)
REVERT: B  293 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7493 (pp20)
REVERT: B  407 ASP cc_start: 0.7146 (m-30) cc_final: 0.6912 (m-30)
REVERT: B  412 HIS cc_start: 0.5544 (OUTLIER) cc_final: 0.5077 (p90)
REVERT: B  479 THR cc_start: 0.9142 (t) cc_final: 0.8875 (m)
REVERT: B  481 ILE cc_start: 0.9270 (mm) cc_final: 0.9030 (mm)
REVERT: B  959 TRP cc_start: 0.7065 (p-90) cc_final: 0.6305 (p-90)
REVERT: B 1078 HIS cc_start: 0.6101 (OUTLIER) cc_final: 0.4844 (m-70)
REVERT: C   47 LEU cc_start: 0.4538 (OUTLIER) cc_final: 0.3978 (tm)
REVERT: C  179 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6444 (pt)
REVERT: C  210 PHE cc_start: 0.5040 (OUTLIER) cc_final: 0.4691 (t80)
  outliers start: 69
  outliers final: 47
  residues processed: 210
  average time/residue: 0.2516
  time to fit residues: 81.5766
Evaluate side-chains
  195 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 141
  time to evaluate  : 1.199 
-------------------------------------------------------------------------------
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 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   56 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  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  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  711 LEU
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  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  135 LEU
Chi-restraints excluded: chain C residue  153 THR
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:    0.0270
   chunk 108 optimal weight:    4.9990
   chunk 115 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9990
   chunk 126 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0000
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.8046

-------------------------------------------------------------------------------
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 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 285 HIS
B 834 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.168473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.144678 restraints weight = 16757.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.140045 restraints weight = 26553.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.137900 restraints weight = 26278.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  13133  Z= 0.126
  Angle     :  0.548   9.203  17880  Z= 0.283
  Chirality :  0.043   0.307   1926
  Planarity :  0.004   0.038   2346
  Dihedral  :  6.332  57.332   1781
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 16.05 %
    Favored  : 79.34 %
  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: -1.35 (0.21), residues: 1620
  helix: -0.83 (0.32), residues: 248
  sheet: -0.96 (0.29), residues: 315
  loop : -0.87 (0.19), residues: 1057

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 179 
 HIS   0.005   0.001   HIS B  78 
 PHE   0.014   0.001   PHE B1010 
 TYR   0.016   0.001   TYR B 309 
 ARG   0.002   0.000   ARG A1456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03583 (  303)
  hydrogen bonds       : angle       5.61995 (  846)
  metal coordination   : bond        0.00161 (    3)
  SS BOND              : bond        0.00341 (   42)
  SS BOND              : angle       1.70046 (   84)
  covalent geometry    : bond        0.00301 (13088)
  covalent geometry    : angle       0.53623 (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
  214 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 148
  time to evaluate  : 1.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1384 TRP cc_start: 0.3412 (OUTLIER) cc_final: 0.2983 (m-90)
REVERT: A 1455 GLU cc_start: 0.7351 (tm-30) cc_final: 0.6845 (tm-30)
REVERT: B  112 LEU cc_start: 0.8321 (mm) cc_final: 0.8095 (mm)
REVERT: B  175 HIS cc_start: 0.7585 (OUTLIER) cc_final: 0.7172 (m-70)
REVERT: B  285 HIS cc_start: 0.5455 (t70) cc_final: 0.4944 (t-90)
REVERT: B  293 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7493 (pp20)
REVERT: B  407 ASP cc_start: 0.7129 (m-30) cc_final: 0.6927 (m-30)
REVERT: B  412 HIS cc_start: 0.5662 (OUTLIER) cc_final: 0.5165 (p90)
REVERT: B  479 THR cc_start: 0.9107 (t) cc_final: 0.8825 (m)
REVERT: B  481 ILE cc_start: 0.9267 (mm) cc_final: 0.9054 (mm)
REVERT: B 1078 HIS cc_start: 0.6147 (OUTLIER) cc_final: 0.5016 (m-70)
REVERT: C   47 LEU cc_start: 0.4532 (OUTLIER) cc_final: 0.3946 (tm)
REVERT: C  179 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6444 (pt)
REVERT: C  194 GLN cc_start: 0.5523 (OUTLIER) cc_final: 0.5280 (mm-40)
REVERT: C  210 PHE cc_start: 0.4971 (OUTLIER) cc_final: 0.4667 (t80)
  outliers start: 66
  outliers final: 47
  residues processed: 203
  average time/residue: 0.2462
  time to fit residues: 75.0338
Evaluate side-chains
  194 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 138
  time to evaluate  : 1.333 
-------------------------------------------------------------------------------
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 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 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   56 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  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  488 LEU
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  669 VAL
Chi-restraints excluded: chain B residue  674 LYS
Chi-restraints excluded: chain B residue  711 LEU
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  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   52 GLU
Chi-restraints excluded: chain C residue   88 PHE
Chi-restraints excluded: chain C residue  153 THR
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:    6.9990
   chunk 118 optimal weight:    0.1980
   chunk 104 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 64 optimal weight:    0.7980
   chunk 122 optimal weight:    0.9990
   chunk 139 optimal weight:    8.9990
   chunk 73 optimal weight:   10.0000
   chunk 81 optimal weight:    3.9990
   chunk 157 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   overall best weight:    1.5986

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.166192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.142674 restraints weight = 17007.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.138148 restraints weight = 25859.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.135297 restraints weight = 30669.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073  13133  Z= 0.190
  Angle     :  0.583  10.750  17880  Z= 0.303
  Chirality :  0.045   0.265   1926
  Planarity :  0.004   0.039   2346
  Dihedral  :  6.479  58.253   1779
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 17.03 %
    Favored  : 78.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.21), residues: 1620
  helix: -0.69 (0.34), residues: 242
  sheet: -1.07 (0.30), residues: 306
  loop : -0.91 (0.19), residues: 1072

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 959 
 HIS   0.007   0.001   HIS B 492 
 PHE   0.018   0.002   PHE B 912 
 TYR   0.014   0.002   TYR B 776 
 ARG   0.003   0.000   ARG B 972 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03697 (  303)
  hydrogen bonds       : angle       5.62240 (  846)
  metal coordination   : bond        0.00254 (    3)
  SS BOND              : bond        0.00460 (   42)
  SS BOND              : angle       1.45938 (   84)
  covalent geometry    : bond        0.00456 (13088)
  covalent geometry    : angle       0.57559 (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
  219 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 149
  time to evaluate  : 1.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1384 TRP cc_start: 0.3581 (OUTLIER) cc_final: 0.3161 (m-90)
REVERT: B  112 LEU cc_start: 0.8372 (mm) cc_final: 0.7951 (mt)
REVERT: B  285 HIS cc_start: 0.5672 (t70) cc_final: 0.5148 (t-90)
REVERT: B  293 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7508 (pp20)
REVERT: B  407 ASP cc_start: 0.7087 (m-30) cc_final: 0.6869 (m-30)
REVERT: B  412 HIS cc_start: 0.5723 (OUTLIER) cc_final: 0.5259 (p90)
REVERT: B  481 ILE cc_start: 0.9269 (mm) cc_final: 0.9026 (mm)
REVERT: B  959 TRP cc_start: 0.7094 (p-90) cc_final: 0.6720 (p-90)
REVERT: B  962 ILE cc_start: 0.8750 (mm) cc_final: 0.8320 (mm)
REVERT: B 1078 HIS cc_start: 0.6110 (OUTLIER) cc_final: 0.4933 (m-70)
REVERT: C   47 LEU cc_start: 0.4589 (OUTLIER) cc_final: 0.4042 (tm)
REVERT: C  179 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6407 (pt)
REVERT: C  210 PHE cc_start: 0.5104 (OUTLIER) cc_final: 0.4757 (t80)
  outliers start: 70
  outliers final: 52
  residues processed: 208
  average time/residue: 0.2406
  time to fit residues: 76.0261
Evaluate side-chains
  203 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 144
  time to evaluate  : 1.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1159 THR
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 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 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   56 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  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  488 LEU
Chi-restraints excluded: chain B residue  497 ILE
Chi-restraints excluded: chain B residue  550 THR
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  674 LYS
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  717 THR
Chi-restraints excluded: chain B residue  808 VAL
Chi-restraints excluded: chain B residue  833 LEU
Chi-restraints excluded: chain B residue  845 THR
Chi-restraints excluded: chain B residue  852 SER
Chi-restraints excluded: chain B residue  858 VAL
Chi-restraints excluded: chain B residue  899 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   47 LEU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   52 GLU
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain C residue   88 PHE
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:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 93 optimal weight:    0.6980
   chunk 154 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 144 optimal weight:    7.9990
   chunk 129 optimal weight:    1.9990
   chunk 157 optimal weight:    2.9990
   chunk 21 optimal weight:   10.0000
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 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 584 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.166867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.143342 restraints weight = 16722.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.138642 restraints weight = 26122.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.136090 restraints weight = 27987.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078  13133  Z= 0.168
  Angle     :  0.582  13.767  17880  Z= 0.302
  Chirality :  0.044   0.258   1926
  Planarity :  0.004   0.038   2346
  Dihedral  :  6.411  57.692   1776
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 18.07 %
    Favored  : 77.18 %
  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 (0.21), residues: 1620
  helix: -0.64 (0.34), residues: 236
  sheet: -1.12 (0.30), residues: 311
  loop : -0.89 (0.19), residues: 1073

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 179 
 HIS   0.006   0.001   HIS B 492 
 PHE   0.017   0.001   PHE B 912 
 TYR   0.014   0.001   TYR B 776 
 ARG   0.002   0.000   ARG C 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03577 (  303)
  hydrogen bonds       : angle       5.50155 (  846)
  metal coordination   : bond        0.00262 (    3)
  SS BOND              : bond        0.00447 (   42)
  SS BOND              : angle       1.46718 (   84)
  covalent geometry    : bond        0.00402 (13088)
  covalent geometry    : angle       0.57467 (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
  215 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 147
  time to evaluate  : 1.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1193 LYS cc_start: 0.7050 (mmtm) cc_final: 0.6795 (mmtp)
REVERT: A 1384 TRP cc_start: 0.3691 (OUTLIER) cc_final: 0.3219 (m-90)
REVERT: B  112 LEU cc_start: 0.8417 (mm) cc_final: 0.7988 (mt)
REVERT: B  285 HIS cc_start: 0.5704 (t70) cc_final: 0.5194 (t-90)
REVERT: B  293 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7499 (pp20)
REVERT: B  407 ASP cc_start: 0.7054 (m-30) cc_final: 0.6840 (m-30)
REVERT: B  412 HIS cc_start: 0.5748 (OUTLIER) cc_final: 0.5269 (p90)
REVERT: B  481 ILE cc_start: 0.9245 (mm) cc_final: 0.9026 (mm)
REVERT: B  959 TRP cc_start: 0.7021 (p-90) cc_final: 0.6766 (p-90)
REVERT: B 1078 HIS cc_start: 0.6113 (OUTLIER) cc_final: 0.4882 (m-70)
REVERT: C   47 LEU cc_start: 0.4680 (OUTLIER) cc_final: 0.4190 (tm)
REVERT: C  109 CYS cc_start: 0.4054 (t) cc_final: 0.3826 (t)
REVERT: C  179 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6380 (pt)
REVERT: C  194 GLN cc_start: 0.5405 (OUTLIER) cc_final: 0.5116 (mm-40)
REVERT: C  210 PHE cc_start: 0.5100 (OUTLIER) cc_final: 0.4765 (t80)
  outliers start: 68
  outliers final: 58
  residues processed: 204
  average time/residue: 0.2231
  time to fit residues: 68.8667
Evaluate side-chains
  207 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 141
  time to evaluate  : 1.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1159 THR
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 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   56 VAL
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  175 HIS
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  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  550 THR
Chi-restraints excluded: chain B residue  587 GLN
Chi-restraints excluded: chain B residue  669 VAL
Chi-restraints excluded: chain B residue  674 LYS
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  717 THR
Chi-restraints excluded: chain B residue  721 THR
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  852 SER
Chi-restraints excluded: chain B residue  858 VAL
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   47 LEU
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain C residue   88 PHE
Chi-restraints excluded: chain C residue  135 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 163
   random chunks:
   chunk 135 optimal weight:    9.9990
   chunk 149 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 88 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9980
   chunk 137 optimal weight:    4.9990
   chunk 99 optimal weight:    1.9990
   chunk 117 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 109 optimal weight:    3.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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 153 GLN
** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 350 HIS
** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.164217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.138976 restraints weight = 16973.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.135111 restraints weight = 28885.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.133860 restraints weight = 30410.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.071  13133  Z= 0.249
  Angle     :  0.641  14.061  17880  Z= 0.334
  Chirality :  0.046   0.234   1926
  Planarity :  0.004   0.038   2346
  Dihedral  :  6.720  59.011   1776
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 18.28 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.21), residues: 1620
  helix: -0.81 (0.34), residues: 236
  sheet: -1.06 (0.30), residues: 308
  loop : -1.01 (0.19), residues: 1076

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 842 
 HIS   0.007   0.001   HIS B 492 
 PHE   0.021   0.002   PHE B 912 
 TYR   0.015   0.002   TYR B 776 
 ARG   0.003   0.000   ARG B 972 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03898 (  303)
  hydrogen bonds       : angle       5.72481 (  846)
  metal coordination   : bond        0.00454 (    3)
  SS BOND              : bond        0.00528 (   42)
  SS BOND              : angle       1.60990 (   84)
  covalent geometry    : bond        0.00592 (13088)
  covalent geometry    : angle       0.63253 (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
  219 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 147
  time to evaluate  : 1.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1193 LYS cc_start: 0.7136 (mmtm) cc_final: 0.6892 (mmtp)
REVERT: A 1384 TRP cc_start: 0.3629 (OUTLIER) cc_final: 0.3075 (m-90)
REVERT: B  112 LEU cc_start: 0.8387 (mm) cc_final: 0.7971 (mt)
REVERT: B  285 HIS cc_start: 0.5690 (t70) cc_final: 0.5174 (t-90)
REVERT: B  293 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7547 (pp20)
REVERT: B  407 ASP cc_start: 0.7095 (m-30) cc_final: 0.6864 (m-30)
REVERT: B  412 HIS cc_start: 0.5991 (OUTLIER) cc_final: 0.5477 (p90)
REVERT: B  481 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.9017 (mm)
REVERT: B  831 MET cc_start: 0.8136 (mpp) cc_final: 0.7435 (mpp)
REVERT: B  959 TRP cc_start: 0.7157 (p-90) cc_final: 0.6856 (p-90)
REVERT: C  109 CYS cc_start: 0.4483 (t) cc_final: 0.4218 (t)
REVERT: C  179 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6410 (pt)
REVERT: C  210 PHE cc_start: 0.5160 (OUTLIER) cc_final: 0.4756 (t80)
  outliers start: 72
  outliers final: 61
  residues processed: 204
  average time/residue: 0.2956
  time to fit residues: 91.3182
Evaluate side-chains
  207 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 140
  time to evaluate  : 2.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1159 THR
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 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   56 VAL
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  139 THR
Chi-restraints excluded: chain B residue  175 HIS
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  425 LEU
Chi-restraints excluded: chain B residue  473 MET
Chi-restraints excluded: chain B residue  481 ILE
Chi-restraints excluded: chain B residue  488 LEU
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  674 LYS
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  717 THR
Chi-restraints excluded: chain B residue  721 THR
Chi-restraints excluded: chain B residue  741 VAL
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  852 SER
Chi-restraints excluded: chain B residue  858 VAL
Chi-restraints excluded: chain B residue  882 ASP
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   52 GLU
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain C residue   88 PHE
Chi-restraints excluded: chain C residue  135 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  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:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 122 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 112 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0570
   chunk 5 optimal weight:    0.8980
   chunk 74 optimal weight:   10.0000
   chunk 50 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 87 optimal weight:    0.6980
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
B  83 GLN
** 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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.169026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.144235 restraints weight = 16667.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.139502 restraints weight = 27991.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.137904 restraints weight = 27787.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068  13133  Z= 0.120
  Angle     :  0.554  12.665  17880  Z= 0.287
  Chirality :  0.043   0.223   1926
  Planarity :  0.004   0.038   2346
  Dihedral  :  6.265  56.045   1774
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 19.05 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.21), residues: 1620
  helix: -0.65 (0.34), residues: 242
  sheet: -0.98 (0.30), residues: 308
  loop : -0.87 (0.20), residues: 1070

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 210 
 HIS   0.004   0.001   HIS B 492 
 PHE   0.011   0.001   PHE A1516 
 TYR   0.012   0.001   TYR B 776 
 ARG   0.003   0.000   ARG A1313 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03344 (  303)
  hydrogen bonds       : angle       5.37781 (  846)
  metal coordination   : bond        0.00061 (    3)
  SS BOND              : bond        0.00402 (   42)
  SS BOND              : angle       1.32227 (   84)
  covalent geometry    : bond        0.00288 (13088)
  covalent geometry    : angle       0.54818 (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
  216 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 152
  time to evaluate  : 1.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1169 GLN cc_start: 0.6536 (mm-40) cc_final: 0.5756 (mm-40)
REVERT: A 1193 LYS cc_start: 0.7070 (mmtm) cc_final: 0.6819 (mmtp)
REVERT: A 1384 TRP cc_start: 0.3650 (OUTLIER) cc_final: 0.3209 (m-90)
REVERT: A 1466 TYR cc_start: 0.3542 (OUTLIER) cc_final: 0.3304 (t80)
REVERT: B  112 LEU cc_start: 0.8353 (mm) cc_final: 0.8076 (mt)
REVERT: B  285 HIS cc_start: 0.5300 (t70) cc_final: 0.4823 (t-90)
REVERT: B  293 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7568 (pp20)
REVERT: B  309 TYR cc_start: 0.9053 (m-10) cc_final: 0.8557 (m-10)
REVERT: B  412 HIS cc_start: 0.5576 (OUTLIER) cc_final: 0.5113 (p90)
REVERT: B  565 ASP cc_start: 0.6914 (t0) cc_final: 0.6603 (t0)
REVERT: B  959 TRP cc_start: 0.6989 (p-90) cc_final: 0.6293 (p-90)
REVERT: B  962 ILE cc_start: 0.8537 (mm) cc_final: 0.8198 (mm)
REVERT: B 1078 HIS cc_start: 0.6182 (OUTLIER) cc_final: 0.5034 (m-70)
REVERT: C  179 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6347 (pt)
REVERT: C  194 GLN cc_start: 0.5510 (OUTLIER) cc_final: 0.4982 (mm-40)
REVERT: C  210 PHE cc_start: 0.5097 (OUTLIER) cc_final: 0.4734 (t80)
  outliers start: 64
  outliers final: 47
  residues processed: 204
  average time/residue: 0.3140
  time to fit residues: 97.1529
Evaluate side-chains
  198 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 143
  time to evaluate  : 1.786 
-------------------------------------------------------------------------------
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 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 1466 TYR
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  175 HIS
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  488 LEU
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  669 VAL
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  717 THR
Chi-restraints excluded: chain B residue  721 THR
Chi-restraints excluded: chain B residue  808 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 1065 ILE
Chi-restraints excluded: chain B residue 1078 HIS
Chi-restraints excluded: chain B residue 1107 VAL
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain C residue   88 PHE
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  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:    3.9990
   chunk 124 optimal weight:    0.6980
   chunk 56 optimal weight:    6.9990
   chunk 90 optimal weight:    0.8980
   chunk 9 optimal weight:    6.9990
   chunk 106 optimal weight:    0.9990
   chunk 140 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 82 optimal weight:    3.9990
   chunk 149 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A1236 HIS
** 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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.164174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.139108 restraints weight = 16866.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.136053 restraints weight = 30133.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.134271 restraints weight = 30192.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064  13133  Z= 0.241
  Angle     :  0.641  13.426  17880  Z= 0.334
  Chirality :  0.046   0.226   1926
  Planarity :  0.004   0.038   2346
  Dihedral  :  6.639  58.129   1774
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 19.19 %
    Favored  : 76.41 %
  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: -1.50 (0.21), residues: 1620
  helix: -0.71 (0.34), residues: 235
  sheet: -1.14 (0.30), residues: 309
  loop : -1.02 (0.19), residues: 1076

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  44 
 HIS   0.007   0.001   HIS B 492 
 PHE   0.021   0.002   PHE B 912 
 TYR   0.015   0.002   TYR B 776 
 ARG   0.008   0.000   ARG A1456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03747 (  303)
  hydrogen bonds       : angle       5.67871 (  846)
  metal coordination   : bond        0.00436 (    3)
  SS BOND              : bond        0.00501 (   42)
  SS BOND              : angle       1.73695 (   84)
  covalent geometry    : bond        0.00575 (13088)
  covalent geometry    : angle       0.63090 (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
  201 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 138
  time to evaluate  : 1.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1169 GLN cc_start: 0.6440 (mm-40) cc_final: 0.5501 (mm-40)
REVERT: A 1193 LYS cc_start: 0.7154 (mmtm) cc_final: 0.6905 (mmtp)
REVERT: A 1384 TRP cc_start: 0.3627 (OUTLIER) cc_final: 0.3095 (m-90)
REVERT: A 1466 TYR cc_start: 0.3817 (OUTLIER) cc_final: 0.3492 (t80)
REVERT: B  112 LEU cc_start: 0.8429 (mm) cc_final: 0.8002 (mt)
REVERT: B  285 HIS cc_start: 0.5597 (t70) cc_final: 0.5120 (t-90)
REVERT: B  293 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7571 (pp20)
REVERT: B  309 TYR cc_start: 0.9017 (m-10) cc_final: 0.8515 (m-10)
REVERT: B  412 HIS cc_start: 0.5851 (OUTLIER) cc_final: 0.5365 (p90)
REVERT: B  959 TRP cc_start: 0.6998 (p-90) cc_final: 0.6298 (p-90)
REVERT: B 1078 HIS cc_start: 0.6071 (OUTLIER) cc_final: 0.4828 (m-70)
REVERT: C  179 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6408 (pt)
REVERT: C  210 PHE cc_start: 0.5244 (OUTLIER) cc_final: 0.4843 (t80)
  outliers start: 63
  outliers final: 53
  residues processed: 191
  average time/residue: 0.3227
  time to fit residues: 95.0891
Evaluate side-chains
  195 residues out of total 1433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 135
  time to evaluate  : 1.776 
-------------------------------------------------------------------------------
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 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 1466 TYR
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 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   56 VAL
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  175 HIS
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  488 LEU
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  669 VAL
Chi-restraints excluded: chain B residue  674 LYS
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  717 THR
Chi-restraints excluded: chain B residue  721 THR
Chi-restraints excluded: chain B residue  741 VAL
Chi-restraints excluded: chain B residue  808 VAL
Chi-restraints excluded: chain B residue  845 THR
Chi-restraints excluded: chain B residue  858 VAL
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 B residue 1107 VAL
Chi-restraints excluded: chain C residue   52 GLU
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain C residue   88 PHE
Chi-restraints excluded: chain C residue  135 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  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:    0.0980
   chunk 125 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 122 optimal weight:    2.9990
   chunk 108 optimal weight:    1.9990
   chunk 107 optimal weight:    0.6980
   chunk 94 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 142 optimal weight:    2.9990
   chunk 141 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A1236 HIS
** 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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.168654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.143963 restraints weight = 16622.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.139919 restraints weight = 27715.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.138160 restraints weight = 30140.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.2435

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= 0.118
  Angle     :  0.555  12.257  17880  Z= 0.288
  Chirality :  0.043   0.213   1926
  Planarity :  0.004   0.038   2346
  Dihedral  :  6.258  56.402   1774
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 19.68 %
    Favored  : 76.41 %
  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: -1.22 (0.21), residues: 1620
  helix: -0.54 (0.34), residues: 241
  sheet: -0.87 (0.30), residues: 297
  loop : -0.85 (0.20), residues: 1082

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 210 
 HIS   0.005   0.001   HIS B  78 
 PHE   0.012   0.001   PHE B 306 
 TYR   0.012   0.001   TYR B 776 
 ARG   0.003   0.000   ARG A1456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03292 (  303)
  hydrogen bonds       : angle       5.32386 (  846)
  metal coordination   : bond        0.00157 (    3)
  SS BOND              : bond        0.00441 (   42)
  SS BOND              : angle       1.28104 (   84)
  covalent geometry    : bond        0.00283 (13088)
  covalent geometry    : angle       0.54963 (17796)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5137.61 seconds
wall clock time: 95 minutes 55.03 seconds (5755.03 seconds total)