Starting phenix.real_space_refine
on Mon Dec 30 09:43:21 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7whv_32512/12_2024/7whv_32512.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7whv_32512/12_2024/7whv_32512.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7whv_32512/12_2024/7whv_32512.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7whv_32512/12_2024/7whv_32512.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7whv_32512/12_2024/7whv_32512.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7whv_32512/12_2024/7whv_32512.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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: 8
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     Mg      1      5.21       5
     S      60      5.16       5
     Be      1      3.05       5
     C    7953      2.51       5
     N    2033      2.21       5
     O    2278      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 12331
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1158, 9249
          Classifications: {'peptide': 1158}
          Link IDs: {'PTRANS': 39, 'TRANS': 1118}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2934
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 19, 'TRANS': 342}
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 109
          Unusual residues: {' MG': 1, '6PL': 2, 'BEF': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 7.43, per 1000 atoms: 0.60
  Number of scatterers: 12331
  At special positions: 0
  Unit cell: (150.87, 97.37, 132.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     S      60     16.00
     P       2     15.00
     Mg      1     11.99
     F       3      9.00
     O    2278      8.00
     N    2033      7.00
     C    7953      6.00
     Be      1      4.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 110 " - pdb=" SG  CYS B 159 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 216 " - pdb=" SG  CYS B 231 " distance=2.01

  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=1, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
    NAG-ASN
      " NAG C   1 " - " ASN B 240 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.14
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2848

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 11 sheets defined
      44.1% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 205 through 215
    Processing helix  chain 'A' and resid 217 through 229
      removed outlier: 3.665A  pdb=" N   VAL A 221 " --> pdb=" O   ASN A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 243
      No H-bonds generated for 'chain 'A' and resid 241 through 243'
    Processing helix  chain 'A' and resid 244 through 274
      removed outlier: 3.809A  pdb=" N   ARG A 265 " --> pdb=" O   GLU A 261 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   LEU A 268 " --> pdb=" O   ARG A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 401
    Processing helix  chain 'A' and resid 452 through 456
      removed outlier: 4.419A  pdb=" N   THR A 455 " --> pdb=" O   CYS A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 464
      removed outlier: 3.772A  pdb=" N   ARG A 464 " --> pdb=" O   LYS A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 503
      No H-bonds generated for 'chain 'A' and resid 501 through 503'
    Processing helix  chain 'A' and resid 525 through 528
    Processing helix  chain 'A' and resid 529 through 534
    Processing helix  chain 'A' and resid 543 through 576
      removed outlier: 4.272A  pdb=" N   ASN A 550 " --> pdb=" O   SER A 546 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   PHE A 551 " --> pdb=" O   ARG A 547 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ASP A 576 " --> pdb=" O   GLY A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 609
      removed outlier: 3.523A  pdb=" N   ILE A 607 " --> pdb=" O   TRP A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 613
    Processing helix  chain 'A' and resid 615 through 634
      removed outlier: 4.647A  pdb=" N   ILE A 619 " --> pdb=" O   ILE A 615 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 639
      removed outlier: 3.774A  pdb=" N   LEU A 638 " --> pdb=" O   ASP A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 656 through 659
    Processing helix  chain 'A' and resid 708 through 725
    Processing helix  chain 'A' and resid 762 through 777
      removed outlier: 3.546A  pdb=" N   MET A 771 " --> pdb=" O   CYS A 767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 798 through 811
    Processing helix  chain 'A' and resid 892 through 906
    Processing helix  chain 'A' and resid 921 through 936
      removed outlier: 3.690A  pdb=" N   ALA A 933 " --> pdb=" O   LYS A 929 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 942 through 952
      removed outlier: 3.614A  pdb=" N   ALA A 948 " --> pdb=" O   LEU A 944 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ILE A 951 " --> pdb=" O   VAL A 947 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLU A 952 " --> pdb=" O   ALA A 948 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 981
    Processing helix  chain 'A' and resid 992 through 1003
    Processing helix  chain 'A' and resid 1035 through 1048
      removed outlier: 3.564A  pdb=" N   LYS A1039 " --> pdb=" O   ALA A1035 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   TYR A1040 " --> pdb=" O   LEU A1036 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ASN A1046 " --> pdb=" O   LYS A1042 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   LEU A1047 " --> pdb=" O   GLU A1043 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1056 through 1060
    Processing helix  chain 'A' and resid 1074 through 1080
      removed outlier: 3.778A  pdb=" N   LEU A1079 " --> pdb=" O   ASP A1075 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1083 through 1097
      removed outlier: 3.691A  pdb=" N   LYS A1089 " --> pdb=" O   ASP A1085 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1106 through 1121
    Processing helix  chain 'A' and resid 1131 through 1133
      No H-bonds generated for 'chain 'A' and resid 1131 through 1133'
    Processing helix  chain 'A' and resid 1134 through 1141
    Processing helix  chain 'A' and resid 1153 through 1158
    Processing helix  chain 'A' and resid 1167 through 1174
      removed outlier: 4.302A  pdb=" N   ARG A1171 " --> pdb=" O   ARG A1167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1175 through 1200
      Proline residue:  A1189  - end of helix
      removed outlier: 4.359A  pdb=" N   PHE A1198 " --> pdb=" O   LYS A1194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1200 through 1205
    Processing helix  chain 'A' and resid 1218 through 1225
    Processing helix  chain 'A' and resid 1230 through 1239
      removed outlier: 4.258A  pdb=" N   VAL A1234 " --> pdb=" O   THR A1230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1247 through 1252
    Processing helix  chain 'A' and resid 1253 through 1255
      No H-bonds generated for 'chain 'A' and resid 1253 through 1255'
    Processing helix  chain 'A' and resid 1256 through 1261
    Processing helix  chain 'A' and resid 1266 through 1293
      Proline residue:  A1288  - end of helix
    Processing helix  chain 'A' and resid 1307 through 1330
      removed outlier: 3.698A  pdb=" N   TYR A1326 " --> pdb=" O   SER A1322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1335 through 1357
      removed outlier: 3.551A  pdb=" N   SER A1345 " --> pdb=" O   PHE A1341 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   VAL A1349 " --> pdb=" O   SER A1345 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   PHE A1350 " --> pdb=" O   CYS A1346 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   THR A1353 " --> pdb=" O   VAL A1349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1358 through 1363
      removed outlier: 6.659A  pdb=" N   ALA A1361 " --> pdb=" O   SER A1358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1367 through 1372
    Processing helix  chain 'A' and resid 1375 through 1404
      removed outlier: 3.871A  pdb=" N   TRP A1379 " --> pdb=" O   ALA A1375 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   PHE A1383 " --> pdb=" O   TRP A1379 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   VAL A1384 " --> pdb=" O   ALA A1380 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU A1387 " --> pdb=" O   PHE A1383 " (cutoff:3.500A)
      Proline residue:  A1392  - end of helix
      removed outlier: 3.500A  pdb=" N   PHE A1403 " --> pdb=" O   PHE A1399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1406 through 1418
    Processing helix  chain 'B' and resid 71 through 99
      Proline residue:  B  77  - end of helix
      removed outlier: 3.825A  pdb=" N   LYS B  99 " --> pdb=" O   ALA B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 114
      removed outlier: 3.619A  pdb=" N   ALA B 114 " --> pdb=" O   CYS B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 186 through 191
      removed outlier: 3.880A  pdb=" N   LEU B 191 " --> pdb=" O   ARG B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 199
    Processing helix  chain 'B' and resid 204 through 210
    Processing helix  chain 'B' and resid 231 through 237
      removed outlier: 4.377A  pdb=" N   ALA B 235 " --> pdb=" O   CYS B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 273
      removed outlier: 4.118A  pdb=" N   ARG B 272 " --> pdb=" O   SER B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 290
      removed outlier: 3.559A  pdb=" N   GLU B 290 " --> pdb=" O   PRO B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 315
    Processing helix  chain 'B' and resid 350 through 354
    Processing helix  chain 'B' and resid 372 through 399
    Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 172
    Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 280
    Processing sheet with id=AA3, first strand: chain 'A' and resid 406 through 410
      removed outlier: 6.531A  pdb=" N   TRP A 517 " --> pdb=" O   THR A 424 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   THR A 424 " --> pdb=" O   TRP A 517 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   MET A 519 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ASP A 418 " --> pdb=" O   MET A 523 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 430 through 434
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1011 through 1014
      removed outlier: 3.785A  pdb=" N   ALA A1099 " --> pdb=" O   TYR A1068 " (cutoff:3.500A)
      removed outlier: 7.050A  pdb=" N   LEU A 985 " --> pdb=" O   VAL A1100 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   CYS A1102 " --> pdb=" O   LEU A 985 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   VAL A 987 " --> pdb=" O   CYS A1102 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   GLU A 662 " --> pdb=" O   LYS A 984 " (cutoff:3.500A)
      removed outlier: 7.284A  pdb=" N   TRP A 986 " --> pdb=" O   GLU A 662 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   ILE A 664 " --> pdb=" O   TRP A 986 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   LEU A 988 " --> pdb=" O   ILE A 664 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 687 through 689
      removed outlier: 7.003A  pdb=" N   ARG A 966 " --> pdb=" O   GLN A 674 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   VAL A 676 " --> pdb=" O   GLU A 964 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   GLU A 964 " --> pdb=" O   VAL A 676 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   GLU A 678 " --> pdb=" O   ALA A 962 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   ALA A 962 " --> pdb=" O   GLU A 678 " (cutoff:3.500A)
      removed outlier: 9.340A  pdb=" N   LYS A 680 " --> pdb=" O   GLY A 960 " (cutoff:3.500A)
      removed outlier: 11.795A  pdb=" N   GLY A 960 " --> pdb=" O   LYS A 680 " (cutoff:3.500A)
      removed outlier: 10.108A  pdb=" N   CYS A 682 " --> pdb=" O   LEU A 958 " (cutoff:3.500A)
      removed outlier: 11.613A  pdb=" N   LEU A 958 " --> pdb=" O   CYS A 682 " (cutoff:3.500A)
      removed outlier: 11.199A  pdb=" N   ILE A 684 " --> pdb=" O   ILE A 956 " (cutoff:3.500A)
      removed outlier: 13.879A  pdb=" N   ILE A 956 " --> pdb=" O   ILE A 684 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   ILE A 913 " --> pdb=" O   LEU A 958 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   GLY A 960 " --> pdb=" O   LEU A 911 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   LEU A 911 " --> pdb=" O   GLY A 960 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   ALA A 962 " --> pdb=" O   ARG A 909 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   ARG A 909 " --> pdb=" O   ALA A 962 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   SER A 850 " --> pdb=" O   ILE A 839 " (cutoff:3.500A)
      removed outlier: 4.701A  pdb=" N   ILE A 839 " --> pdb=" O   SER A 850 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ILE A 852 " --> pdb=" O   LEU A 837 " (cutoff:3.500A)
      removed outlier: 4.684A  pdb=" N   GLU A 835 " --> pdb=" O   LYS A 854 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE A 830 " --> pdb=" O   MET A 827 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   GLY A 822 " --> pdb=" O   LYS A 818 " (cutoff:3.500A)
      removed outlier: 4.793A  pdb=" N   LYS A 818 " --> pdb=" O   GLY A 822 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   ILE A 824 " --> pdb=" O   VAL A 816 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 781 through 784
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1128 through 1129
      removed outlier: 3.629A  pdb=" N   ILE A1147 " --> pdb=" O   GLY A1129 " (cutoff:3.500A)
      removed outlier: 6.078A  pdb=" N   GLY A1146 " --> pdb=" O   ILE A1163 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 126 through 129
      removed outlier: 6.219A  pdb=" N   TYR B 177 " --> pdb=" O   LEU B 326 " (cutoff:3.500A)
      removed outlier: 5.662A  pdb=" N   LEU B 326 " --> pdb=" O   TYR B 177 " (cutoff:3.500A)
      removed outlier: 7.403A  pdb=" N   LEU B 179 " --> pdb=" O   THR B 324 " (cutoff:3.500A)
      removed outlier: 5.444A  pdb=" N   THR B 324 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 119 through 120
      removed outlier: 5.841A  pdb=" N   ASP B 343 " --> pdb=" O   GLN B 246 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   GLN B 246 " --> pdb=" O   ASP B 343 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 227 through 228
      removed outlier: 6.121A  pdb=" N   ILE B 227 " --> pdb=" O   ALA B 284 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2

    517 hydrogen bonds defined for protein.
    1461 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: 4.43

  Time building geometry restraints manager: 3.58 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 2113
        1.31 -     1.44: 3404
        1.44 -     1.56: 6999
        1.56 -     1.68: 5
        1.68 -     1.81: 92
  Bond restraints: 12613
  Sorted by residual:
  bond pdb=" F3  BEF A1602 "
       pdb="BE   BEF A1602 "
    ideal  model  delta    sigma   weight residual
    1.476  1.757 -0.281 2.00e-02 2.50e+03 1.98e+02
  bond pdb=" F2  BEF A1602 "
       pdb="BE   BEF A1602 "
    ideal  model  delta    sigma   weight residual
    1.476  1.754 -0.278 2.00e-02 2.50e+03 1.93e+02
  bond pdb=" F1  BEF A1602 "
       pdb="BE   BEF A1602 "
    ideal  model  delta    sigma   weight residual
    1.476  1.745 -0.269 2.00e-02 2.50e+03 1.81e+02
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.326  0.080 2.00e-02 2.50e+03 1.60e+01
  bond pdb=" CG1 ILE A1321 "
       pdb=" CD1 ILE A1321 "
    ideal  model  delta    sigma   weight residual
    1.513  1.362  0.151 3.90e-02 6.57e+02 1.51e+01
  ... (remaining 12608 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.53: 16121
        2.53 -     5.05: 819
        5.05 -     7.58: 117
        7.58 -    10.10: 24
       10.10 -    12.63: 8
  Bond angle restraints: 17089
  Sorted by residual:
  angle pdb=" N   ILE A 706 "
        pdb=" CA  ILE A 706 "
        pdb=" C   ILE A 706 "
      ideal   model   delta    sigma   weight residual
     112.29  105.60    6.69 9.40e-01 1.13e+00 5.07e+01
  angle pdb=" C   TYR B 229 "
        pdb=" N   PRO B 230 "
        pdb=" CA  PRO B 230 "
      ideal   model   delta    sigma   weight residual
     119.84  111.34    8.50 1.25e+00 6.40e-01 4.63e+01
  angle pdb=" CA  TRP A 398 "
        pdb=" CB  TRP A 398 "
        pdb=" CG  TRP A 398 "
      ideal   model   delta    sigma   weight residual
     113.60  126.23  -12.63 1.90e+00 2.77e-01 4.42e+01
  angle pdb=" C   ASN B 279 "
        pdb=" N   TYR B 280 "
        pdb=" CA  TYR B 280 "
      ideal   model   delta    sigma   weight residual
     126.86  135.51   -8.65 1.57e+00 4.06e-01 3.03e+01
  angle pdb=" N   ILE B 403 "
        pdb=" CA  ILE B 403 "
        pdb=" C   ILE B 403 "
      ideal   model   delta    sigma   weight residual
     111.91  107.33    4.58 8.90e-01 1.26e+00 2.65e+01
  ... (remaining 17084 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.58: 7298
       22.58 -    45.16: 221
       45.16 -    67.74: 25
       67.74 -    90.32: 6
       90.32 -   112.90: 4
  Dihedral angle restraints: 7554
    sinusoidal: 3116
      harmonic: 4438
  Sorted by residual:
  dihedral pdb=" CA  ASN B 240 "
           pdb=" C   ASN B 240 "
           pdb=" N   ASP B 241 "
           pdb=" CA  ASP B 241 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.93  -34.07     0      5.00e+00 4.00e-02 4.64e+01
  dihedral pdb=" CA  ASN B 279 "
           pdb=" C   ASN B 279 "
           pdb=" N   TYR B 280 "
           pdb=" CA  TYR B 280 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.10  -30.90     0      5.00e+00 4.00e-02 3.82e+01
  dihedral pdb=" CA  PHE A1365 "
           pdb=" C   PHE A1365 "
           pdb=" N   PHE A1366 "
           pdb=" CA  PHE A1366 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.80  -30.20     0      5.00e+00 4.00e-02 3.65e+01
  ... (remaining 7551 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.116: 1662
       0.116 -    0.231: 213
       0.231 -    0.346: 10
       0.346 -    0.462: 4
       0.462 -    0.577: 2
  Chirality restraints: 1891
  Sorted by residual:
  chirality pdb=" CG  LEU A1126 "
            pdb=" CB  LEU A1126 "
            pdb=" CD1 LEU A1126 "
            pdb=" CD2 LEU A1126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.01   -0.58 2.00e-01 2.50e+01 8.33e+00
  chirality pdb=" CB  ILE B 359 "
            pdb=" CA  ILE B 359 "
            pdb=" CG1 ILE B 359 "
            pdb=" CG2 ILE B 359 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.13    0.51 2.00e-01 2.50e+01 6.54e+00
  chirality pdb=" C2  NAG C   1 "
            pdb=" C1  NAG C   1 "
            pdb=" C3  NAG C   1 "
            pdb=" N2  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.06   -0.44 2.00e-01 2.50e+01 4.76e+00
  ... (remaining 1888 not shown)

  Planarity restraints: 2160
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 142 "    0.050 2.00e-02 2.50e+03   4.04e-02 4.08e+01
        pdb=" CG  TRP B 142 "   -0.106 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 142 "    0.048 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 142 "   -0.012 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 142 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 142 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 142 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 142 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 142 "    0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 142 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 398 "   -0.079 2.00e-02 2.50e+03   3.87e-02 3.75e+01
        pdb=" CG  TRP A 398 "    0.082 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 398 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 398 "    0.029 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 398 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 398 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 398 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 398 "   -0.027 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 398 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 398 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 398 "    0.029 2.00e-02 2.50e+03   5.70e-02 3.25e+01
        pdb=" C   PHE B 398 "   -0.099 2.00e-02 2.50e+03
        pdb=" O   PHE B 398 "    0.037 2.00e-02 2.50e+03
        pdb=" N   GLY B 399 "    0.033 2.00e-02 2.50e+03
  ... (remaining 2157 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 308
        2.66 -     3.22: 11659
        3.22 -     3.78: 21253
        3.78 -     4.34: 29104
        4.34 -     4.90: 46479
  Nonbonded interactions: 108803
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 667 "
            pdb="MG    MG A1601 "
     model   vdw
     2.100 2.170
  nonbonded pdb=" OD2 ASP A 667 "
            pdb=" F1  BEF A1602 "
     model   vdw
     2.123 2.990
  nonbonded pdb=" OD1 ASP A1130 "
            pdb=" F1  BEF A1602 "
     model   vdw
     2.141 2.990
  nonbonded pdb=" O   THR A 669 "
            pdb=" F1  BEF A1602 "
     model   vdw
     2.175 2.990
  nonbonded pdb=" O   THR A1353 "
            pdb=" OG  SER A1357 "
     model   vdw
     2.246 3.040
  ... (remaining 108798 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.240
  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:                     29.330
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
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      :  0.016   0.281  12613  Z= 1.049
  Angle     :  1.294  12.629  17089  Z= 0.702
  Chirality :  0.079   0.577   1891
  Planarity :  0.009   0.061   2159
  Dihedral  : 12.087 112.895   4700
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.02 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  3.25 %
    Favored  : 96.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -3.98 (0.17), residues: 1510
  helix: -3.44 (0.13), residues: 601
  sheet: -2.01 (0.30), residues: 192
  loop : -1.94 (0.21), residues: 717

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.106   0.007   TRP B 142 
 HIS   0.013   0.005   HIS B 186 
 PHE   0.060   0.006   PHE B 243 
 TYR   0.046   0.006   TYR B 297 
 ARG   0.018   0.002   ARG A 880 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 269
  time to evaluate  : 1.331 
Fit side-chains
REVERT: A  464 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7598 (mtm180)
REVERT: A  599 PHE cc_start: 0.7186 (t80) cc_final: 0.6929 (t80)
REVERT: A  674 GLN cc_start: 0.8053 (tt0) cc_final: 0.7789 (tt0)
REVERT: A  685 ASN cc_start: 0.7522 (t160) cc_final: 0.7244 (t0)
REVERT: A  715 GLU cc_start: 0.7173 (tp30) cc_final: 0.6972 (tp30)
REVERT: A  765 ARG cc_start: 0.6869 (mmp-170) cc_final: 0.6516 (mmp80)
REVERT: A  782 VAL cc_start: 0.7695 (t) cc_final: 0.7416 (m)
REVERT: A  824 ILE cc_start: 0.8091 (mt) cc_final: 0.7761 (mp)
REVERT: A  827 MET cc_start: 0.7069 (mtp) cc_final: 0.6835 (mtp)
REVERT: A  835 GLU cc_start: 0.7539 (tt0) cc_final: 0.7314 (tt0)
REVERT: A  837 LEU cc_start: 0.8227 (mt) cc_final: 0.8008 (mp)
REVERT: A  840 LEU cc_start: 0.8587 (mt) cc_final: 0.8354 (mt)
REVERT: A  847 LYS cc_start: 0.7603 (mttp) cc_final: 0.7351 (mtpm)
REVERT: A  853 VAL cc_start: 0.8101 (m) cc_final: 0.7720 (p)
REVERT: A  854 LYS cc_start: 0.7406 (tttt) cc_final: 0.7066 (ttpp)
REVERT: A  898 LEU cc_start: 0.8011 (tp) cc_final: 0.7748 (tp)
REVERT: A  973 ASP cc_start: 0.7238 (m-30) cc_final: 0.6958 (m-30)
REVERT: A 1222 MET cc_start: 0.8115 (mtp) cc_final: 0.7798 (mtp)
REVERT: B   54 LYS cc_start: 0.7665 (ttpt) cc_final: 0.7399 (mmtm)
REVERT: B  134 LYS cc_start: 0.7948 (mttt) cc_final: 0.7700 (mttt)
REVERT: B  215 ASN cc_start: 0.8368 (p0) cc_final: 0.8116 (p0)
REVERT: B  290 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6809 (mm-30)
REVERT: B  315 MET cc_start: 0.8712 (mmm) cc_final: 0.8277 (mmm)
  outliers start: 8
  outliers final: 3
  residues processed: 277
  average time/residue: 1.3476
  time to fit residues: 407.4590
Evaluate side-chains
  166 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 163
  time to evaluate  : 1.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain B residue  348 TRP
Chi-restraints excluded: chain B residue  377 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 127 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 118 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0770
   chunk 71 optimal weight:    0.6980
   chunk 88 optimal weight:    0.8980
   chunk 137 optimal weight:    0.8980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 ASN
A 410 HIS
A 411 ASN
A 437 ASN
A 443 ASN
A 475 HIS
A 477 ASN
A 497 ASN
A 556 ASN
** A 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 685 ASN
A 939 ASN
A1004 ASN
A1061 HIS
A1067 ASN
A1176 HIS
A1266 ASN
A1307 HIS
** A1330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  67 ASN
B 155 GLN
B 255 ASN
B 256 ASN

Total number of N/Q/H flips: 21

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  12613  Z= 0.263
  Angle     :  0.706  11.630  17089  Z= 0.373
  Chirality :  0.047   0.324   1891
  Planarity :  0.005   0.050   2159
  Dihedral  :  9.206  63.939   1822
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  :  9.67 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -2.41 (0.19), residues: 1510
  helix: -1.54 (0.17), residues: 624
  sheet: -1.66 (0.32), residues: 193
  loop : -1.48 (0.23), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 142 
 HIS   0.005   0.001   HIS A1330 
 PHE   0.021   0.002   PHE A 206 
 TYR   0.024   0.002   TYR A1289 
 ARG   0.007   0.001   ARG A 193 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 192
  time to evaluate  : 1.185 
Fit side-chains
   revert: symmetry clash
REVERT: A  532 MET cc_start: 0.7080 (mmt) cc_final: 0.6870 (mmt)
REVERT: A  561 PHE cc_start: 0.7884 (t80) cc_final: 0.7678 (t80)
REVERT: A  574 TYR cc_start: 0.7719 (t80) cc_final: 0.7511 (t80)
REVERT: A  674 GLN cc_start: 0.8193 (tt0) cc_final: 0.7901 (tt0)
REVERT: A  677 MET cc_start: 0.7958 (tpp) cc_final: 0.7724 (tpp)
REVERT: A  715 GLU cc_start: 0.7381 (tp30) cc_final: 0.6996 (tp30)
REVERT: A  765 ARG cc_start: 0.6658 (mmp-170) cc_final: 0.6400 (mmp80)
REVERT: A  768 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6798 (mt-10)
REVERT: A  824 ILE cc_start: 0.7899 (mt) cc_final: 0.7599 (mp)
REVERT: A  827 MET cc_start: 0.7267 (mtp) cc_final: 0.6922 (mtp)
REVERT: A  835 GLU cc_start: 0.7598 (tt0) cc_final: 0.7324 (tt0)
REVERT: A  837 LEU cc_start: 0.7679 (mt) cc_final: 0.7417 (mp)
REVERT: A  847 LYS cc_start: 0.7510 (mttp) cc_final: 0.7253 (mtpm)
REVERT: A  913 ILE cc_start: 0.7769 (mm) cc_final: 0.7431 (tp)
REVERT: A  956 ILE cc_start: 0.7721 (mm) cc_final: 0.7518 (pt)
REVERT: A 1187 MET cc_start: 0.7735 (ttp) cc_final: 0.7008 (tmt)
REVERT: B   54 LYS cc_start: 0.7814 (ttpt) cc_final: 0.7578 (mmpt)
REVERT: B   80 LEU cc_start: 0.7703 (mt) cc_final: 0.7391 (tp)
REVERT: B   96 GLN cc_start: 0.7228 (mp-120) cc_final: 0.6625 (tt0)
REVERT: B  215 ASN cc_start: 0.8177 (p0) cc_final: 0.7948 (p0)
REVERT: B  307 ASP cc_start: 0.7071 (OUTLIER) cc_final: 0.6579 (p0)
REVERT: B  315 MET cc_start: 0.8727 (mmm) cc_final: 0.8393 (mmm)
  outliers start: 46
  outliers final: 21
  residues processed: 228
  average time/residue: 1.2097
  time to fit residues: 302.4784
Evaluate side-chains
  175 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 153
  time to evaluate  : 1.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 THR
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  601 SER
Chi-restraints excluded: chain A residue  655 SER
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  814 SER
Chi-restraints excluded: chain A residue  851 CYS
Chi-restraints excluded: chain A residue 1036 LEU
Chi-restraints excluded: chain A residue 1137 MET
Chi-restraints excluded: chain A residue 1194 LYS
Chi-restraints excluded: chain A residue 1234 VAL
Chi-restraints excluded: chain A residue 1398 SER
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  187 ARG
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  348 TRP
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  403 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 114 optimal weight:    0.6980
   chunk 93 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 137 optimal weight:    2.9990
   chunk 148 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9980
   chunk 136 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 110 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 497 ASN
** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 556 ASN
** A 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1096 ASN
A1330 HIS
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 255 ASN
B 363 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.086  12613  Z= 0.299
  Angle     :  0.676  11.836  17089  Z= 0.353
  Chirality :  0.047   0.326   1891
  Planarity :  0.004   0.048   2159
  Dihedral  :  8.310  56.391   1822
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 11.63 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -1.60 (0.21), residues: 1510
  helix: -0.55 (0.20), residues: 617
  sheet: -1.54 (0.33), residues: 203
  loop : -1.27 (0.24), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 142 
 HIS   0.007   0.001   HIS A1330 
 PHE   0.021   0.002   PHE A1198 
 TYR   0.031   0.002   TYR A 172 
 ARG   0.007   0.001   ARG A 193 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 166
  time to evaluate  : 1.383 
Fit side-chains
REVERT: A  189 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6717 (tmt)
REVERT: A  532 MET cc_start: 0.7177 (mmt) cc_final: 0.6751 (mmt)
REVERT: A  574 TYR cc_start: 0.7771 (t80) cc_final: 0.7552 (t80)
REVERT: A  642 LYS cc_start: 0.8187 (tttt) cc_final: 0.7869 (ttpt)
REVERT: A  674 GLN cc_start: 0.8241 (tt0) cc_final: 0.7964 (tt0)
REVERT: A  677 MET cc_start: 0.7973 (tpp) cc_final: 0.7737 (tpp)
REVERT: A  715 GLU cc_start: 0.7359 (tp30) cc_final: 0.7109 (tp30)
REVERT: A  765 ARG cc_start: 0.6776 (mmp-170) cc_final: 0.6453 (mmp80)
REVERT: A  768 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6608 (mt-10)
REVERT: A  792 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7734 (pp)
REVERT: A  827 MET cc_start: 0.7279 (mtp) cc_final: 0.7004 (mtp)
REVERT: A  835 GLU cc_start: 0.7671 (tt0) cc_final: 0.7382 (tt0)
REVERT: A  840 LEU cc_start: 0.8587 (mt) cc_final: 0.7992 (mt)
REVERT: A  846 ARG cc_start: 0.6149 (mtp85) cc_final: 0.5947 (mtp180)
REVERT: A  847 LYS cc_start: 0.7555 (mttp) cc_final: 0.7297 (mtpm)
REVERT: A  898 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7284 (mm)
REVERT: A  913 ILE cc_start: 0.7908 (mm) cc_final: 0.7661 (tp)
REVERT: A  915 GLN cc_start: 0.8210 (pt0) cc_final: 0.7900 (pt0)
REVERT: A 1187 MET cc_start: 0.7997 (ttp) cc_final: 0.7529 (tmt)
REVERT: A 1215 TYR cc_start: 0.8505 (m-80) cc_final: 0.8251 (m-80)
REVERT: B   54 LYS cc_start: 0.7828 (ttpt) cc_final: 0.7496 (mmtm)
REVERT: B   80 LEU cc_start: 0.7687 (mt) cc_final: 0.7375 (tp)
REVERT: B   96 GLN cc_start: 0.7284 (mp-120) cc_final: 0.6724 (tt0)
REVERT: B  196 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6805 (m-30)
REVERT: B  292 MET cc_start: 0.7530 (tpp) cc_final: 0.6754 (ttm)
REVERT: B  307 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6700 (p0)
REVERT: B  315 MET cc_start: 0.8849 (mmm) cc_final: 0.8373 (mmm)
REVERT: B  333 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7238 (p0)
  outliers start: 53
  outliers final: 25
  residues processed: 202
  average time/residue: 1.2897
  time to fit residues: 285.1067
Evaluate side-chains
  175 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 144
  time to evaluate  : 1.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  405 ASP
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  601 SER
Chi-restraints excluded: chain A residue  655 SER
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  814 SER
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  851 CYS
Chi-restraints excluded: chain A residue  868 LEU
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  989 THR
Chi-restraints excluded: chain A residue 1070 ILE
Chi-restraints excluded: chain A residue 1137 MET
Chi-restraints excluded: chain A residue 1234 VAL
Chi-restraints excluded: chain A residue 1266 ASN
Chi-restraints excluded: chain B residue  102 GLU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  187 ARG
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain B residue  334 THR
Chi-restraints excluded: chain B residue  348 TRP
Chi-restraints excluded: chain B residue  403 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 135 optimal weight:    1.9990
   chunk 103 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 65 optimal weight:    5.9990
   chunk 92 optimal weight:    0.9980
   chunk 137 optimal weight:    1.9990
   chunk 145 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9990
   chunk 130 optimal weight:    0.0670
   chunk 39 optimal weight:    0.0970
   overall best weight:    0.4716

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

Flipped N/Q/H residues before XYZ refinement:
** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 255 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  12613  Z= 0.219
  Angle     :  0.615  11.932  17089  Z= 0.321
  Chirality :  0.045   0.340   1891
  Planarity :  0.004   0.052   2159
  Dihedral  :  7.809  59.564   1821
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 12.99 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -1.21 (0.21), residues: 1510
  helix: -0.12 (0.20), residues: 635
  sheet: -1.23 (0.34), residues: 195
  loop : -1.23 (0.24), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1352 
 HIS   0.003   0.001   HIS A 475 
 PHE   0.019   0.002   PHE A1198 
 TYR   0.027   0.002   TYR A 172 
 ARG   0.008   0.000   ARG A 193 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 162
  time to evaluate  : 1.464 
Fit side-chains
   revert: symmetry clash
REVERT: A  532 MET cc_start: 0.7031 (mmt) cc_final: 0.6677 (mmp)
REVERT: A  574 TYR cc_start: 0.7837 (t80) cc_final: 0.7583 (t80)
REVERT: A  642 LYS cc_start: 0.8162 (tttt) cc_final: 0.7873 (ttpt)
REVERT: A  674 GLN cc_start: 0.8178 (tt0) cc_final: 0.7966 (tt0)
REVERT: A  677 MET cc_start: 0.7923 (tpp) cc_final: 0.7688 (tpp)
REVERT: A  715 GLU cc_start: 0.7324 (tp30) cc_final: 0.7017 (tp30)
REVERT: A  765 ARG cc_start: 0.6845 (mmp-170) cc_final: 0.6561 (mmp80)
REVERT: A  768 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6666 (mt-10)
REVERT: A  792 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7697 (pp)
REVERT: A  827 MET cc_start: 0.7285 (mtp) cc_final: 0.7005 (mtp)
REVERT: A  835 GLU cc_start: 0.7655 (tt0) cc_final: 0.7133 (tt0)
REVERT: A  840 LEU cc_start: 0.8572 (mt) cc_final: 0.8070 (mt)
REVERT: A  846 ARG cc_start: 0.6131 (mtp85) cc_final: 0.5910 (mtp180)
REVERT: A  847 LYS cc_start: 0.7541 (mttp) cc_final: 0.7293 (mtpm)
REVERT: A  894 GLU cc_start: 0.5794 (mp0) cc_final: 0.5555 (mp0)
REVERT: A  898 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7196 (mm)
REVERT: A 1151 GLU cc_start: 0.7963 (pm20) cc_final: 0.7755 (pm20)
REVERT: A 1187 MET cc_start: 0.8037 (ttp) cc_final: 0.7342 (tmt)
REVERT: A 1215 TYR cc_start: 0.8480 (m-80) cc_final: 0.8227 (m-80)
REVERT: B   54 LYS cc_start: 0.7801 (ttpt) cc_final: 0.7470 (mmpt)
REVERT: B   80 LEU cc_start: 0.7652 (mt) cc_final: 0.7348 (tp)
REVERT: B   96 GLN cc_start: 0.7234 (mp-120) cc_final: 0.6650 (tt0)
REVERT: B  307 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6736 (p0)
REVERT: B  333 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7159 (p0)
  outliers start: 51
  outliers final: 22
  residues processed: 198
  average time/residue: 1.2397
  time to fit residues: 269.2654
Evaluate side-chains
  171 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 145
  time to evaluate  : 1.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  405 ASP
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  575 TYR
Chi-restraints excluded: chain A residue  601 SER
Chi-restraints excluded: chain A residue  655 SER
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue 1073 ASP
Chi-restraints excluded: chain A residue 1137 MET
Chi-restraints excluded: chain A residue 1234 VAL
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  187 ARG
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain B residue  334 THR
Chi-restraints excluded: chain B residue  348 TRP
Chi-restraints excluded: chain B residue  403 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 121 optimal weight:    2.9990
   chunk 82 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 108 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 124 optimal weight:    0.5980
   chunk 100 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   chunk 131 optimal weight:    0.5980
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 194 ASN
** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 550 ASN
A1266 ASN
A1416 GLN
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 255 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  12613  Z= 0.252
  Angle     :  0.625  11.895  17089  Z= 0.325
  Chirality :  0.045   0.333   1891
  Planarity :  0.004   0.054   2159
  Dihedral  :  7.736  57.426   1821
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 13.60 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.21), residues: 1510
  helix:  0.17 (0.21), residues: 625
  sheet: -1.20 (0.34), residues: 199
  loop : -1.13 (0.24), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 314 
 HIS   0.003   0.001   HIS B 347 
 PHE   0.020   0.002   PHE A1198 
 TYR   0.028   0.002   TYR A 172 
 ARG   0.009   0.001   ARG A 193 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 158
  time to evaluate  : 1.427 
Fit side-chains
REVERT: A  532 MET cc_start: 0.7083 (mmt) cc_final: 0.6777 (mmp)
REVERT: A  574 TYR cc_start: 0.7886 (t80) cc_final: 0.7627 (t80)
REVERT: A  674 GLN cc_start: 0.8179 (tt0) cc_final: 0.7924 (tt0)
REVERT: A  677 MET cc_start: 0.7886 (tpp) cc_final: 0.7622 (tpp)
REVERT: A  765 ARG cc_start: 0.6799 (mmp-170) cc_final: 0.6520 (mmp80)
REVERT: A  768 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6668 (mt-10)
REVERT: A  792 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7697 (pp)
REVERT: A  827 MET cc_start: 0.7293 (mtp) cc_final: 0.7067 (mtp)
REVERT: A  835 GLU cc_start: 0.7547 (tt0) cc_final: 0.7142 (tt0)
REVERT: A  840 LEU cc_start: 0.8581 (mt) cc_final: 0.8161 (mt)
REVERT: A  846 ARG cc_start: 0.6117 (mtp85) cc_final: 0.5799 (mtp180)
REVERT: A  847 LYS cc_start: 0.7565 (mttp) cc_final: 0.7308 (mtpm)
REVERT: A  898 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7150 (mm)
REVERT: A 1109 GLN cc_start: 0.7154 (mt0) cc_final: 0.6933 (mt0)
REVERT: A 1187 MET cc_start: 0.8165 (ttp) cc_final: 0.7491 (tmt)
REVERT: A 1215 TYR cc_start: 0.8552 (m-80) cc_final: 0.8314 (m-80)
REVERT: B   54 LYS cc_start: 0.7808 (ttpt) cc_final: 0.7463 (mmpt)
REVERT: B   62 ARG cc_start: 0.7898 (mmt90) cc_final: 0.7681 (mmt90)
REVERT: B   80 LEU cc_start: 0.7669 (mt) cc_final: 0.7373 (tp)
REVERT: B   96 GLN cc_start: 0.7238 (mp-120) cc_final: 0.6701 (tt0)
REVERT: B  196 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.6960 (m-30)
REVERT: B  292 MET cc_start: 0.7520 (tpp) cc_final: 0.6796 (ttm)
REVERT: B  307 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6860 (p0)
REVERT: B  333 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7211 (p0)
  outliers start: 55
  outliers final: 28
  residues processed: 197
  average time/residue: 1.2599
  time to fit residues: 272.5432
Evaluate side-chains
  183 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 150
  time to evaluate  : 1.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  575 TYR
Chi-restraints excluded: chain A residue  601 SER
Chi-restraints excluded: chain A residue  655 SER
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  868 LEU
Chi-restraints excluded: chain A residue  876 ILE
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue 1073 ASP
Chi-restraints excluded: chain A residue 1137 MET
Chi-restraints excluded: chain A residue 1234 VAL
Chi-restraints excluded: chain A residue 1398 SER
Chi-restraints excluded: chain A residue 1406 THR
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  102 GLU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  151 ASP
Chi-restraints excluded: chain B residue  187 ARG
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain B residue  334 THR
Chi-restraints excluded: chain B residue  348 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 131 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0270
   chunk 85 optimal weight:    0.3980
   chunk 36 optimal weight:    0.5980
   chunk 146 optimal weight:    2.9990
   chunk 121 optimal weight:    2.9990
   chunk 67 optimal weight:    7.9990
   chunk 12 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 255 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.3024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  12613  Z= 0.213
  Angle     :  0.599  11.859  17089  Z= 0.311
  Chirality :  0.044   0.344   1891
  Planarity :  0.004   0.055   2159
  Dihedral  :  7.548  58.885   1821
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 14.12 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.21), residues: 1510
  helix:  0.31 (0.21), residues: 624
  sheet: -1.02 (0.35), residues: 193
  loop : -1.11 (0.24), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1352 
 HIS   0.003   0.001   HIS A 475 
 PHE   0.019   0.002   PHE A1198 
 TYR   0.029   0.002   TYR A 172 
 ARG   0.008   0.000   ARG A 193 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 156
  time to evaluate  : 1.338 
Fit side-chains
REVERT: A  532 MET cc_start: 0.7115 (mmt) cc_final: 0.6826 (mmp)
REVERT: A  574 TYR cc_start: 0.7889 (t80) cc_final: 0.7605 (t80)
REVERT: A  677 MET cc_start: 0.7824 (tpp) cc_final: 0.7547 (tpp)
REVERT: A  715 GLU cc_start: 0.6704 (pp20) cc_final: 0.6497 (pp20)
REVERT: A  765 ARG cc_start: 0.6789 (mmp-170) cc_final: 0.6503 (mmp80)
REVERT: A  768 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6657 (mt-10)
REVERT: A  792 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7690 (pp)
REVERT: A  827 MET cc_start: 0.7253 (mtp) cc_final: 0.6988 (mtp)
REVERT: A  835 GLU cc_start: 0.7544 (tt0) cc_final: 0.7122 (tt0)
REVERT: A  846 ARG cc_start: 0.6063 (mtp85) cc_final: 0.5789 (mtp180)
REVERT: A  847 LYS cc_start: 0.7595 (mttp) cc_final: 0.7327 (mtpm)
REVERT: A  894 GLU cc_start: 0.5824 (mp0) cc_final: 0.5566 (mp0)
REVERT: A  898 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7124 (mm)
REVERT: A 1109 GLN cc_start: 0.7110 (mt0) cc_final: 0.6899 (mt0)
REVERT: A 1187 MET cc_start: 0.8155 (ttp) cc_final: 0.7417 (tmt)
REVERT: A 1215 TYR cc_start: 0.8542 (m-80) cc_final: 0.8321 (m-80)
REVERT: B   54 LYS cc_start: 0.7796 (ttpt) cc_final: 0.7456 (mmpt)
REVERT: B   80 LEU cc_start: 0.7683 (mt) cc_final: 0.7382 (tp)
REVERT: B   96 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6682 (tt0)
REVERT: B  196 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6822 (m-30)
REVERT: B  292 MET cc_start: 0.7589 (tpp) cc_final: 0.6796 (ttm)
REVERT: B  307 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6910 (p0)
  outliers start: 59
  outliers final: 25
  residues processed: 197
  average time/residue: 1.2606
  time to fit residues: 272.3706
Evaluate side-chains
  176 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 146
  time to evaluate  : 1.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  575 TYR
Chi-restraints excluded: chain A residue  601 SER
Chi-restraints excluded: chain A residue  655 SER
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  868 LEU
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  913 ILE
Chi-restraints excluded: chain A residue 1073 ASP
Chi-restraints excluded: chain A residue 1137 MET
Chi-restraints excluded: chain A residue 1234 VAL
Chi-restraints excluded: chain A residue 1398 SER
Chi-restraints excluded: chain A residue 1406 THR
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   96 GLN
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  187 ARG
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  334 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 140 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 83 optimal weight:    0.6980
   chunk 106 optimal weight:    0.6980
   chunk 82 optimal weight:    3.9990
   chunk 122 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 145 optimal weight:    0.1980
   chunk 91 optimal weight:    0.8980
   chunk 88 optimal weight:    2.9990
   chunk 67 optimal weight:    8.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1266 ASN
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 255 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  12613  Z= 0.262
  Angle     :  0.631  11.715  17089  Z= 0.326
  Chirality :  0.045   0.337   1891
  Planarity :  0.004   0.058   2159
  Dihedral  :  7.548  55.701   1819
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 14.20 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.21), residues: 1510
  helix:  0.32 (0.21), residues: 627
  sheet: -1.12 (0.34), residues: 199
  loop : -1.14 (0.24), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 314 
 HIS   0.003   0.001   HIS B 347 
 PHE   0.020   0.002   PHE A1198 
 TYR   0.032   0.002   TYR A 172 
 ARG   0.010   0.001   ARG B  62 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 158
  time to evaluate  : 1.372 
Fit side-chains
   revert: symmetry clash
REVERT: A  532 MET cc_start: 0.7082 (mmt) cc_final: 0.6837 (mmp)
REVERT: A  574 TYR cc_start: 0.7912 (t80) cc_final: 0.7622 (t80)
REVERT: A  677 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7569 (tpp)
REVERT: A  765 ARG cc_start: 0.6739 (mmp-170) cc_final: 0.6452 (mmp80)
REVERT: A  768 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6669 (mt-10)
REVERT: A  792 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7704 (pp)
REVERT: A  827 MET cc_start: 0.7250 (mtp) cc_final: 0.6994 (mtp)
REVERT: A  835 GLU cc_start: 0.7354 (tt0) cc_final: 0.6941 (tt0)
REVERT: A  846 ARG cc_start: 0.5965 (mtp85) cc_final: 0.5732 (mtp180)
REVERT: A  847 LYS cc_start: 0.7596 (mttp) cc_final: 0.7340 (mtpm)
REVERT: A  898 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7134 (mm)
REVERT: A 1036 LEU cc_start: 0.5660 (pt) cc_final: 0.5171 (OUTLIER)
REVERT: A 1109 GLN cc_start: 0.7143 (mt0) cc_final: 0.6927 (mt0)
REVERT: A 1187 MET cc_start: 0.8183 (ttp) cc_final: 0.7233 (tmt)
REVERT: A 1215 TYR cc_start: 0.8548 (m-80) cc_final: 0.8301 (m-80)
REVERT: B   54 LYS cc_start: 0.7815 (ttpt) cc_final: 0.7499 (tptt)
REVERT: B   80 LEU cc_start: 0.7708 (mt) cc_final: 0.7394 (tp)
REVERT: B   96 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6755 (tt0)
REVERT: B  196 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.6968 (m-30)
REVERT: B  292 MET cc_start: 0.7589 (tpp) cc_final: 0.6788 (ttm)
REVERT: B  307 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6924 (p0)
  outliers start: 60
  outliers final: 30
  residues processed: 203
  average time/residue: 1.2105
  time to fit residues: 270.3738
Evaluate side-chains
  183 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 148
  time to evaluate  : 1.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  575 TYR
Chi-restraints excluded: chain A residue  601 SER
Chi-restraints excluded: chain A residue  655 SER
Chi-restraints excluded: chain A residue  677 MET
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  868 LEU
Chi-restraints excluded: chain A residue  876 ILE
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  913 ILE
Chi-restraints excluded: chain A residue 1073 ASP
Chi-restraints excluded: chain A residue 1137 MET
Chi-restraints excluded: chain A residue 1398 SER
Chi-restraints excluded: chain A residue 1406 THR
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   96 GLN
Chi-restraints excluded: chain B residue  102 GLU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  187 ARG
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  334 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 90 optimal weight:    0.9990
   chunk 58 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   chunk 13 optimal weight:    4.9990
   chunk 114 optimal weight:    6.9990
   chunk 132 optimal weight:    1.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.2965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.100  12613  Z= 0.419
  Angle     :  0.730  11.926  17089  Z= 0.378
  Chirality :  0.049   0.318   1891
  Planarity :  0.004   0.059   2159
  Dihedral  :  8.091  57.104   1819
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 15.41 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.21), residues: 1510
  helix:  0.17 (0.20), residues: 624
  sheet: -1.30 (0.34), residues: 204
  loop : -1.19 (0.24), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 314 
 HIS   0.005   0.002   HIS A 475 
 PHE   0.025   0.003   PHE A1198 
 TYR   0.042   0.003   TYR A 172 
 ARG   0.014   0.001   ARG B  62 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 150
  time to evaluate  : 1.437 
Fit side-chains
REVERT: A  392 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7908 (pttm)
REVERT: A  454 ASN cc_start: 0.6959 (m-40) cc_final: 0.6679 (m110)
REVERT: A  532 MET cc_start: 0.7216 (mmt) cc_final: 0.6930 (mmp)
REVERT: A  574 TYR cc_start: 0.7929 (t80) cc_final: 0.7626 (t80)
REVERT: A  677 MET cc_start: 0.7967 (tpp) cc_final: 0.7756 (tpp)
REVERT: A  765 ARG cc_start: 0.6675 (mmp-170) cc_final: 0.6417 (mmp80)
REVERT: A  768 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6700 (mt-10)
REVERT: A  792 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7677 (pp)
REVERT: A  801 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6702 (mp0)
REVERT: A  827 MET cc_start: 0.7366 (mtp) cc_final: 0.7105 (mtp)
REVERT: A  835 GLU cc_start: 0.7281 (tt0) cc_final: 0.6865 (tt0)
REVERT: A  840 LEU cc_start: 0.8550 (mp) cc_final: 0.7983 (mt)
REVERT: A  846 ARG cc_start: 0.6120 (mtp85) cc_final: 0.5821 (mtp180)
REVERT: A  847 LYS cc_start: 0.7712 (mttp) cc_final: 0.7456 (mtpm)
REVERT: A  898 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7215 (mm)
REVERT: A 1036 LEU cc_start: 0.5728 (pt) cc_final: 0.5268 (pp)
REVERT: A 1187 MET cc_start: 0.8215 (ttp) cc_final: 0.7667 (tmt)
REVERT: A 1215 TYR cc_start: 0.8570 (m-80) cc_final: 0.8290 (m-80)
REVERT: B   54 LYS cc_start: 0.7919 (ttpt) cc_final: 0.7602 (tptt)
REVERT: B   80 LEU cc_start: 0.7718 (mt) cc_final: 0.7421 (tp)
REVERT: B   96 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.6825 (tt0)
REVERT: B  138 THR cc_start: 0.7498 (p) cc_final: 0.7147 (t)
REVERT: B  196 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.7040 (m-30)
REVERT: B  292 MET cc_start: 0.7591 (tpp) cc_final: 0.6769 (ttm)
REVERT: B  307 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.6954 (p0)
  outliers start: 54
  outliers final: 30
  residues processed: 190
  average time/residue: 1.2498
  time to fit residues: 260.5454
Evaluate side-chains
  181 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 144
  time to evaluate  : 1.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  575 TYR
Chi-restraints excluded: chain A residue  601 SER
Chi-restraints excluded: chain A residue  655 SER
Chi-restraints excluded: chain A residue  774 LEU
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  801 GLU
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  868 LEU
Chi-restraints excluded: chain A residue  876 ILE
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  913 ILE
Chi-restraints excluded: chain A residue 1073 ASP
Chi-restraints excluded: chain A residue 1137 MET
Chi-restraints excluded: chain A residue 1347 LEU
Chi-restraints excluded: chain A residue 1348 VAL
Chi-restraints excluded: chain A residue 1398 SER
Chi-restraints excluded: chain A residue 1406 THR
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue   96 GLN
Chi-restraints excluded: chain B residue  102 GLU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  187 ARG
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  307 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 139 optimal weight:    0.8980
   chunk 127 optimal weight:    0.9980
   chunk 135 optimal weight:    0.7980
   chunk 81 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0670
   chunk 106 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0980
   chunk 122 optimal weight:    0.8980
   chunk 128 optimal weight:    0.9990
   chunk 89 optimal weight:    0.5980
   chunk 143 optimal weight:    0.8980
   overall best weight:    0.4718

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

Flipped N/Q/H residues before XYZ refinement:
** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 497 ASN
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 255 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.3159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  12613  Z= 0.227
  Angle     :  0.628  12.047  17089  Z= 0.325
  Chirality :  0.045   0.357   1891
  Planarity :  0.004   0.059   2159
  Dihedral  :  7.619  59.422   1819
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 16.31 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.21), residues: 1510
  helix:  0.34 (0.21), residues: 624
  sheet: -1.15 (0.34), residues: 213
  loop : -1.17 (0.24), residues: 673

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1352 
 HIS   0.003   0.001   HIS B 347 
 PHE   0.019   0.002   PHE A1198 
 TYR   0.036   0.002   TYR A 172 
 ARG   0.008   0.000   ARG A 193 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 149
  time to evaluate  : 1.406 
Fit side-chains
REVERT: A  532 MET cc_start: 0.7148 (mmt) cc_final: 0.6836 (mmp)
REVERT: A  574 TYR cc_start: 0.7901 (t80) cc_final: 0.7611 (t80)
REVERT: A  677 MET cc_start: 0.7852 (tpp) cc_final: 0.7596 (tpp)
REVERT: A  706 ILE cc_start: 0.6803 (OUTLIER) cc_final: 0.6387 (mt)
REVERT: A  765 ARG cc_start: 0.6675 (mmp-170) cc_final: 0.6400 (mmp80)
REVERT: A  768 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6662 (mt-10)
REVERT: A  792 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7670 (pp)
REVERT: A  827 MET cc_start: 0.7249 (mtp) cc_final: 0.6937 (mtp)
REVERT: A  835 GLU cc_start: 0.7144 (tt0) cc_final: 0.6767 (tt0)
REVERT: A  840 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8174 (mt)
REVERT: A  846 ARG cc_start: 0.6131 (mtp85) cc_final: 0.5812 (mtp180)
REVERT: A  847 LYS cc_start: 0.7611 (mttp) cc_final: 0.7335 (mtpm)
REVERT: A  898 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7107 (mm)
REVERT: A 1036 LEU cc_start: 0.5632 (pt) cc_final: 0.5271 (pp)
REVERT: A 1187 MET cc_start: 0.8153 (ttp) cc_final: 0.7216 (tmt)
REVERT: A 1215 TYR cc_start: 0.8511 (m-80) cc_final: 0.8271 (m-80)
REVERT: B   54 LYS cc_start: 0.7896 (ttpt) cc_final: 0.7594 (tptt)
REVERT: B   80 LEU cc_start: 0.7708 (mt) cc_final: 0.7397 (tp)
REVERT: B   96 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.6773 (tt0)
REVERT: B  196 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6929 (m-30)
REVERT: B  307 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.7001 (p0)
  outliers start: 45
  outliers final: 28
  residues processed: 181
  average time/residue: 1.1948
  time to fit residues: 237.5308
Evaluate side-chains
  182 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 147
  time to evaluate  : 1.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  470 GLU
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  575 TYR
Chi-restraints excluded: chain A residue  601 SER
Chi-restraints excluded: chain A residue  655 SER
Chi-restraints excluded: chain A residue  706 ILE
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  840 LEU
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  868 LEU
Chi-restraints excluded: chain A residue  876 ILE
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  913 ILE
Chi-restraints excluded: chain A residue 1073 ASP
Chi-restraints excluded: chain A residue 1137 MET
Chi-restraints excluded: chain A residue 1347 LEU
Chi-restraints excluded: chain A residue 1398 SER
Chi-restraints excluded: chain A residue 1406 THR
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   96 GLN
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  187 ARG
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  403 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 68 optimal weight:    0.4980
   chunk 99 optimal weight:    0.6980
   chunk 150 optimal weight:    0.0000
   chunk 138 optimal weight:    0.0980
   chunk 119 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 92 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 95 optimal weight:    0.5980
   chunk 127 optimal weight:    0.7980
   overall best weight:    0.3784

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

Flipped N/Q/H residues before XYZ refinement:
** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 497 ASN
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 255 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.3257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  12613  Z= 0.206
  Angle     :  0.623  12.135  17089  Z= 0.322
  Chirality :  0.044   0.365   1891
  Planarity :  0.004   0.061   2159
  Dihedral  :  7.469  59.644   1819
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.54 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.21), residues: 1510
  helix:  0.45 (0.21), residues: 624
  sheet: -1.07 (0.33), residues: 215
  loop : -1.17 (0.24), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1352 
 HIS   0.006   0.001   HIS A 475 
 PHE   0.018   0.002   PHE A1198 
 TYR   0.033   0.002   TYR A 172 
 ARG   0.009   0.000   ARG A 193 

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 150
  time to evaluate  : 1.437 
Fit side-chains
REVERT: A  189 MET cc_start: 0.6673 (OUTLIER) cc_final: 0.6465 (tmt)
REVERT: A  532 MET cc_start: 0.7127 (mmt) cc_final: 0.6788 (mmp)
REVERT: A  574 TYR cc_start: 0.7885 (t80) cc_final: 0.7592 (t80)
REVERT: A  677 MET cc_start: 0.7852 (tpp) cc_final: 0.7591 (tpp)
REVERT: A  706 ILE cc_start: 0.6844 (OUTLIER) cc_final: 0.6402 (mt)
REVERT: A  738 GLN cc_start: 0.3812 (pp30) cc_final: 0.3309 (pm20)
REVERT: A  765 ARG cc_start: 0.6662 (mmp-170) cc_final: 0.6389 (mmp80)
REVERT: A  768 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6739 (mt-10)
REVERT: A  792 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7665 (pp)
REVERT: A  835 GLU cc_start: 0.7039 (tt0) cc_final: 0.6770 (tt0)
REVERT: A  840 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.7985 (mt)
REVERT: A  846 ARG cc_start: 0.6096 (mtp85) cc_final: 0.5780 (mtp180)
REVERT: A  847 LYS cc_start: 0.7546 (mttp) cc_final: 0.7240 (mtpm)
REVERT: A  898 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7113 (mm)
REVERT: A 1036 LEU cc_start: 0.5412 (pt) cc_final: 0.5078 (pp)
REVERT: A 1187 MET cc_start: 0.8151 (ttp) cc_final: 0.7206 (tmt)
REVERT: A 1215 TYR cc_start: 0.8546 (m-80) cc_final: 0.8310 (m-80)
REVERT: B   54 LYS cc_start: 0.7807 (ttpt) cc_final: 0.7493 (tptt)
REVERT: B   80 LEU cc_start: 0.7711 (mt) cc_final: 0.7403 (tp)
REVERT: B   96 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6739 (tt0)
REVERT: B  196 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6794 (m-30)
REVERT: B  292 MET cc_start: 0.7566 (tpp) cc_final: 0.6952 (ttm)
REVERT: B  307 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.6898 (p0)
REVERT: B  388 MET cc_start: 0.5741 (mmp) cc_final: 0.5441 (mmt)
  outliers start: 38
  outliers final: 23
  residues processed: 176
  average time/residue: 1.2444
  time to fit residues: 239.9861
Evaluate side-chains
  176 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 145
  time to evaluate  : 1.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  480 THR
Chi-restraints excluded: chain A residue  575 TYR
Chi-restraints excluded: chain A residue  601 SER
Chi-restraints excluded: chain A residue  655 SER
Chi-restraints excluded: chain A residue  706 ILE
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  840 LEU
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  868 LEU
Chi-restraints excluded: chain A residue  876 ILE
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  913 ILE
Chi-restraints excluded: chain A residue 1073 ASP
Chi-restraints excluded: chain A residue 1137 MET
Chi-restraints excluded: chain A residue 1398 SER
Chi-restraints excluded: chain A residue 1406 THR
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   96 GLN
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  187 ARG
Chi-restraints excluded: chain B residue  196 ASP
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  403 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 36 optimal weight:    0.5980
   chunk 110 optimal weight:    0.5980
   chunk 17 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 119 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 123 optimal weight:    0.4980
   chunk 15 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0060
   chunk 105 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1109 GLN
** B  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 GLN
B 255 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.160845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.132786 restraints weight = 14958.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 1.60
r_work: 0.3435 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3327 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.3313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  12613  Z= 0.221
  Angle     :  0.627  11.973  17089  Z= 0.323
  Chirality :  0.044   0.351   1891
  Planarity :  0.004   0.059   2159
  Dihedral  :  7.420  59.955   1819
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.77 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.22), residues: 1510
  helix:  0.53 (0.21), residues: 621
  sheet: -1.06 (0.33), residues: 211
  loop : -1.08 (0.24), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 487 
 HIS   0.008   0.001   HIS A 475 
 PHE   0.019   0.002   PHE A1198 
 TYR   0.029   0.002   TYR A 172 
 ARG   0.010   0.000   ARG A 496 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4750.67 seconds
wall clock time: 86 minutes 51.73 seconds (5211.73 seconds total)