Starting phenix.real_space_refine
on Thu Jul 31 00:59:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8isi_35691/07_2025/8isi_35691.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8isi_35691/07_2025/8isi_35691.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8isi_35691/07_2025/8isi_35691.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8isi_35691/07_2025/8isi_35691.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8isi_35691/07_2025/8isi_35691.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8isi_35691/07_2025/8isi_35691.cif"
  }
  resolution = 3.77
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     102      5.16       5
     C    8319      2.51       5
     N    2236      2.21       5
     O    2438      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13095
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6581
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 842, 6581
          Classifications: {'peptide': 842}
          Link IDs: {'PTRANS': 32, 'TRANS': 809}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 6514
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 833, 6514
          Classifications: {'peptide': 833}
          Link IDs: {'PTRANS': 32, 'TRANS': 800}
          Chain breaks: 5
  Time building chain proxies: 9.60, per 1000 atoms: 0.73
  Number of scatterers: 13095
  At special positions: 0
  Unit cell: (123.25, 129.2, 132.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     102     16.00
     O    2438      8.00
     N    2236      7.00
     C    8319      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.67
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3144

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 16 sheets defined
      42.9% alpha, 19.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 100 through 108
      removed outlier: 3.579A  pdb=" N   SER A 104 " --> pdb=" O   SER A 100 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   GLU A 105 " --> pdb=" O   GLU A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 146
    Processing helix  chain 'A' and resid 149 through 154
      removed outlier: 4.016A  pdb=" N   ASN A 154 " --> pdb=" O   SER A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 202
    Processing helix  chain 'A' and resid 203 through 205
      No H-bonds generated for 'chain 'A' and resid 203 through 205'
    Processing helix  chain 'A' and resid 206 through 213
    Processing helix  chain 'A' and resid 218 through 235
      removed outlier: 3.509A  pdb=" N   LEU A 222 " --> pdb=" O   SER A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 285
      removed outlier: 3.701A  pdb=" N   LYS A 284 " --> pdb=" O   PHE A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 331
      removed outlier: 3.628A  pdb=" N   TYR A 327 " --> pdb=" O   CYS A 323 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   MET A 328 " --> pdb=" O   HIS A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 424
      removed outlier: 3.530A  pdb=" N   ARG A 384 " --> pdb=" O   PRO A 380 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLU A 403 " --> pdb=" O   ASN A 399 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ASP A 405 " --> pdb=" O   GLU A 401 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLN A 407 " --> pdb=" O   GLU A 403 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   MET A 408 " --> pdb=" O   LEU A 404 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   VAL A 409 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   GLU A 410 " --> pdb=" O   ASN A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 479
    Processing helix  chain 'A' and resid 489 through 494
    Processing helix  chain 'A' and resid 497 through 502
      removed outlier: 3.557A  pdb=" N   LEU A 501 " --> pdb=" O   ARG A 497 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   GLY A 502 " --> pdb=" O   ALA A 498 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 497 through 502'
    Processing helix  chain 'A' and resid 569 through 590
      removed outlier: 3.599A  pdb=" N   MET A 573 " --> pdb=" O   LYS A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 779 through 787
    Processing helix  chain 'A' and resid 789 through 794
    Processing helix  chain 'A' and resid 814 through 831
      removed outlier: 3.727A  pdb=" N   PHE A 818 " --> pdb=" O   ASN A 814 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   THR A 830 " --> pdb=" O   ASN A 826 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 876 through 924
      Proline residue:  A 910  - end of helix
      removed outlier: 3.595A  pdb=" N   THR A 924 " --> pdb=" O   MET A 920 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 927 through 950
    Processing helix  chain 'A' and resid 952 through 959
      removed outlier: 4.294A  pdb=" N   ILE A 956 " --> pdb=" O   ASP A 952 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 969 through 988
      removed outlier: 3.875A  pdb=" N   VAL A 973 " --> pdb=" O   THR A 969 " (cutoff:3.500A)
      removed outlier: 4.873A  pdb=" N   MET A 983 " --> pdb=" O   SER A 979 " (cutoff:3.500A)
      removed outlier: 5.352A  pdb=" N   LYS A 984 " --> pdb=" O   GLN A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 997 through 1003
    Processing helix  chain 'A' and resid 1008 through 1027
      removed outlier: 3.674A  pdb=" N   LEU A1012 " --> pdb=" O   ASP A1008 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1065 through 1073
      removed outlier: 3.748A  pdb=" N   PHE A1073 " --> pdb=" O   LEU A1069 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1080 through 1096
    Processing helix  chain 'B' and resid 101 through 107
    Processing helix  chain 'B' and resid 134 through 147
    Processing helix  chain 'B' and resid 196 through 201
    Processing helix  chain 'B' and resid 204 through 213
      removed outlier: 3.510A  pdb=" N   SER B 213 " --> pdb=" O   THR B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 218 through 235
    Processing helix  chain 'B' and resid 275 through 285
    Processing helix  chain 'B' and resid 322 through 332
      removed outlier: 3.518A  pdb=" N   GLN B 326 " --> pdb=" O   SER B 322 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   TYR B 327 " --> pdb=" O   CYS B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 421
      removed outlier: 3.547A  pdb=" N   ALA B 391 " --> pdb=" O   CYS B 387 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   GLN B 392 " --> pdb=" O   GLU B 388 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL B 393 " --> pdb=" O   PHE B 389 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   CYS B 421 " --> pdb=" O   GLN B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 428 through 435
      removed outlier: 4.330A  pdb=" N   ILE B 432 " --> pdb=" O   ALA B 428 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   VAL B 433 " --> pdb=" O   PRO B 429 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 442
    Processing helix  chain 'B' and resid 464 through 479
    Processing helix  chain 'B' and resid 489 through 494
    Processing helix  chain 'B' and resid 569 through 590
      removed outlier: 3.904A  pdb=" N   MET B 573 " --> pdb=" O   LYS B 569 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 779 through 787
    Processing helix  chain 'B' and resid 789 through 794
      removed outlier: 3.565A  pdb=" N   VAL B 793 " --> pdb=" O   LYS B 789 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 814 through 831
      removed outlier: 3.607A  pdb=" N   PHE B 818 " --> pdb=" O   ASN B 814 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 876 through 893
      removed outlier: 3.926A  pdb=" N   VAL B 885 " --> pdb=" O   GLN B 881 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   GLN B 886 " --> pdb=" O   ALA B 882 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   THR B 892 " --> pdb=" O   LEU B 888 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ALA B 893 " --> pdb=" O   ALA B 889 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 894 through 907
      removed outlier: 3.585A  pdb=" N   LYS B 898 " --> pdb=" O   VAL B 894 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU B 900 " --> pdb=" O   ARG B 896 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   ALA B 901 " --> pdb=" O   LEU B 897 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 907 through 923
      removed outlier: 3.630A  pdb=" N   LEU B 911 " --> pdb=" O   ILE B 907 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 927 through 950
      removed outlier: 3.990A  pdb=" N   ASP B 950 " --> pdb=" O   LYS B 946 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 970 through 988
      removed outlier: 3.611A  pdb=" N   GLN B 980 " --> pdb=" O   ALA B 976 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   VAL B 981 " --> pdb=" O   SER B 977 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   MET B 983 " --> pdb=" O   SER B 979 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   LYS B 984 " --> pdb=" O   GLN B 980 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 997 through 1003
    Processing helix  chain 'B' and resid 1009 through 1025
    Processing helix  chain 'B' and resid 1065 through 1073
    Processing helix  chain 'B' and resid 1080 through 1096
      removed outlier: 3.553A  pdb=" N   SER B1085 " --> pdb=" O   GLU B1081 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU B1086 " --> pdb=" O   GLU B1082 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 99
    Processing sheet with id=AA2, first strand: chain 'A' and resid 238 through 240
      removed outlier: 7.020A  pdb=" N   VAL A 341 " --> pdb=" O   TRP A 366 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   LEU A 368 " --> pdb=" O   MET A 339 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   MET A 339 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   VAL A 370 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   LEU A 337 " --> pdb=" O   VAL A 370 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   HIS A 372 " --> pdb=" O   ALA A 335 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   ALA A 335 " --> pdb=" O   HIS A 372 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 244
    Processing sheet with id=AA4, first strand: chain 'A' and resid 457 through 458
      removed outlier: 3.664A  pdb=" N   TRP A 457 " --> pdb=" O   LEU A 450 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   LEU A 450 " --> pdb=" O   TRP A 457 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLY A 447 " --> pdb=" O   PHE A 522 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   GLY A 484 " --> pdb=" O   THR A 746 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 775 through 778
      removed outlier: 6.238A  pdb=" N   GLY A 768 " --> pdb=" O   THR A 776 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   TRP A 778 " --> pdb=" O   ILE A 766 " (cutoff:3.500A)
      removed outlier: 7.619A  pdb=" N   ILE A 766 " --> pdb=" O   TRP A 778 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   GLY A 867 " --> pdb=" O   LYS A 858 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LYS A 858 " --> pdb=" O   GLY A 867 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 803 through 804
    Processing sheet with id=AA7, first strand: chain 'A' and resid 966 through 968
    Processing sheet with id=AA8, first strand: chain 'A' and resid 991 through 994
      removed outlier: 6.342A  pdb=" N   ARG A 991 " --> pdb=" O   LEU A1033 " (cutoff:3.500A)
      removed outlier: 7.923A  pdb=" N   VAL A1035 " --> pdb=" O   ARG A 991 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   THR A 993 " --> pdb=" O   VAL A1035 " (cutoff:3.500A)
      removed outlier: 8.669A  pdb=" N   ALA A1037 " --> pdb=" O   THR A 993 " (cutoff:3.500A)
      removed outlier: 5.106A  pdb=" N   GLN A1032 " --> pdb=" O   THR A1060 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 79 through 80
      removed outlier: 6.828A  pdb=" N   ALA B  88 " --> pdb=" O   ILE B  97 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   TYR B  99 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   LEU B  86 " --> pdb=" O   TYR B  99 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLU B 183 " --> pdb=" O   TYR B 168 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 250 through 257
      removed outlier: 7.079A  pdb=" N   ALA B 241 " --> pdb=" O   VAL B 253 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   GLU B 255 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   VAL B 239 " --> pdb=" O   GLU B 255 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   TRP B 366 " --> pdb=" O   PHE B 244 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 250 through 257
      removed outlier: 7.079A  pdb=" N   ALA B 241 " --> pdb=" O   VAL B 253 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   GLU B 255 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   VAL B 239 " --> pdb=" O   GLU B 255 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   TRP B 366 " --> pdb=" O   PHE B 244 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   VAL B 341 " --> pdb=" O   TRP B 366 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 455 through 460
      removed outlier: 6.442A  pdb=" N   GLY B 484 " --> pdb=" O   PHE B 745 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 775 through 778
      removed outlier: 6.513A  pdb=" N   GLY B 768 " --> pdb=" O   THR B 776 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   TRP B 778 " --> pdb=" O   ILE B 766 " (cutoff:3.500A)
      removed outlier: 7.242A  pdb=" N   ILE B 766 " --> pdb=" O   TRP B 778 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   GLY B 867 " --> pdb=" O   LYS B 858 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LEU B 852 " --> pdb=" O   GLN B 873 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   VAL B 855 " --> pdb=" O   GLU B 835 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   GLU B 835 " --> pdb=" O   VAL B 855 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 803 through 804
    Processing sheet with id=AB6, first strand: chain 'B' and resid 966 through 969
      removed outlier: 3.768A  pdb=" N   LYS B 966 " --> pdb=" O   GLY B1007 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLY B1007 " --> pdb=" O   LYS B 966 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   PHE B 968 " --> pdb=" O   LEU B1005 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU B1005 " --> pdb=" O   PHE B 968 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'B' and resid 991 through 994
      removed outlier: 4.625A  pdb=" N   GLN B1032 " --> pdb=" O   THR B1060 " (cutoff:3.500A)

    681 hydrogen bonds defined for protein.
    1938 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 6.06

  Time building geometry restraints manager: 4.32 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4082
        1.34 -     1.46: 1893
        1.46 -     1.58: 7189
        1.58 -     1.70: 0
        1.70 -     1.82: 164
  Bond restraints: 13328
  Sorted by residual:
  bond pdb=" N   VAL B 793 "
       pdb=" CA  VAL B 793 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.25e-02 6.40e+03 7.38e+00
  bond pdb=" C   ASN B 758 "
       pdb=" N   PRO B 759 "
    ideal  model  delta    sigma   weight residual
    1.332  1.366 -0.035 1.30e-02 5.92e+03 7.20e+00
  bond pdb=" N   GLU B 105 "
       pdb=" CA  GLU B 105 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.035 1.33e-02 5.65e+03 6.84e+00
  bond pdb=" N   GLY A 533 "
       pdb=" CA  GLY A 533 "
    ideal  model  delta    sigma   weight residual
    1.446  1.477 -0.031 1.23e-02 6.61e+03 6.47e+00
  bond pdb=" N   HIS B 172 "
       pdb=" CA  HIS B 172 "
    ideal  model  delta    sigma   weight residual
    1.455  1.486 -0.031 1.25e-02 6.40e+03 6.06e+00
  ... (remaining 13323 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.66: 17831
        2.66 -     5.31: 141
        5.31 -     7.96: 17
        7.96 -    10.62: 3
       10.62 -    13.27: 1
  Bond angle restraints: 17993
  Sorted by residual:
  angle pdb=" CA  LEU A 430 "
        pdb=" CB  LEU A 430 "
        pdb=" CG  LEU A 430 "
      ideal   model   delta    sigma   weight residual
     116.30  129.57  -13.27 3.50e+00 8.16e-02 1.44e+01
  angle pdb=" CA  LYS B 807 "
        pdb=" CB  LYS B 807 "
        pdb=" CG  LYS B 807 "
      ideal   model   delta    sigma   weight residual
     114.10  121.55   -7.45 2.00e+00 2.50e-01 1.39e+01
  angle pdb=" CA  GLY A 533 "
        pdb=" C   GLY A 533 "
        pdb=" O   GLY A 533 "
      ideal   model   delta    sigma   weight residual
     122.47  118.61    3.86 1.08e+00 8.57e-01 1.28e+01
  angle pdb=" CA  MET B1096 "
        pdb=" CB  MET B1096 "
        pdb=" CG  MET B1096 "
      ideal   model   delta    sigma   weight residual
     114.10  121.21   -7.11 2.00e+00 2.50e-01 1.26e+01
  angle pdb=" C   PRO B 759 "
        pdb=" CA  PRO B 759 "
        pdb=" CB  PRO B 759 "
      ideal   model   delta    sigma   weight residual
     111.46  107.26    4.20 1.29e+00 6.01e-01 1.06e+01
  ... (remaining 17988 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.57: 7217
       17.57 -    35.13: 718
       35.13 -    52.70: 154
       52.70 -    70.27: 25
       70.27 -    87.83: 10
  Dihedral angle restraints: 8124
    sinusoidal: 3281
      harmonic: 4843
  Sorted by residual:
  dihedral pdb=" CA  MET B 518 "
           pdb=" C   MET B 518 "
           pdb=" N   ILE B 519 "
           pdb=" CA  ILE B 519 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.27  -19.73     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  ASP B  90 "
           pdb=" CB  ASP B  90 "
           pdb=" CG  ASP B  90 "
           pdb=" OD1 ASP B  90 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.93   56.93     1      2.00e+01 2.50e-03 1.09e+01
  dihedral pdb=" CA  VAL A 981 "
           pdb=" C   VAL A 981 "
           pdb=" N   MET A 982 "
           pdb=" CA  MET A 982 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.61  -16.39     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 8121 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1581
       0.040 -    0.080: 346
       0.080 -    0.120: 123
       0.120 -    0.161: 19
       0.161 -    0.201: 2
  Chirality restraints: 2071
  Sorted by residual:
  chirality pdb=" CA  VAL B 793 "
            pdb=" N   VAL B 793 "
            pdb=" C   VAL B 793 "
            pdb=" CB  VAL B 793 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CA  HIS B 172 "
            pdb=" N   HIS B 172 "
            pdb=" C   HIS B 172 "
            pdb=" CB  HIS B 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.18e-01
  chirality pdb=" CA  TYR A 385 "
            pdb=" N   TYR A 385 "
            pdb=" C   TYR A 385 "
            pdb=" CB  TYR A 385 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.66e-01
  ... (remaining 2068 not shown)

  Planarity restraints: 2293
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 758 "   -0.011 2.00e-02 2.50e+03   2.24e-02 5.01e+00
        pdb=" C   ASN B 758 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ASN B 758 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   PRO B 759 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 462 "   -0.033 5.00e-02 4.00e+02   5.00e-02 4.01e+00
        pdb=" N   PRO A 463 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A 463 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 463 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 481 "    0.010 2.00e-02 2.50e+03   1.95e-02 3.80e+00
        pdb=" C   ASP A 481 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ASP A 481 "    0.013 2.00e-02 2.50e+03
        pdb=" N   SER A 482 "    0.011 2.00e-02 2.50e+03
  ... (remaining 2290 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 203
        2.68 -     3.24: 12133
        3.24 -     3.79: 19114
        3.79 -     4.35: 24006
        4.35 -     4.90: 40983
  Nonbonded interactions: 96439
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 930 "
            pdb=" OG1 THR B 924 "
     model   vdw
     2.128 3.040
  nonbonded pdb=" OG  SER B 213 "
            pdb=" OE1 GLU B1077 "
     model   vdw
     2.171 3.040
  nonbonded pdb=" O   SER A 104 "
            pdb=" OG1 THR A 108 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" OG  SER A 100 "
            pdb=" OD1 ASN A 102 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" N   GLU A 835 "
            pdb=" OE1 GLU A 835 "
     model   vdw
     2.232 3.120
  ... (remaining 96434 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 75 through 347 or resid 361 through 534 or resid 562 throu \ 
gh 1039 or resid 1052 through 1119))
  selection = (chain 'B' and (resid 75 through 109 or resid 120 through 347 or resid 361 throu \ 
gh 1119))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             25.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.570
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     37.530
  Find NCS groups from input model:        0.670
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   67.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  13328  Z= 0.149
  Angle     :  0.605  13.275  17993  Z= 0.323
  Chirality :  0.040   0.201   2071
  Planarity :  0.004   0.050   2293
  Dihedral  : 14.570  87.835   4980
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  : 14.64 %
    Favored  : 85.29 %
  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:  1.00 (0.22), residues: 1651
  helix:  2.29 (0.20), residues: 667
  sheet:  0.43 (0.28), residues: 362
  loop : -1.04 (0.25), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 521 
 HIS   0.011   0.001   HIS A 172 
 PHE   0.015   0.001   PHE A 869 
 TYR   0.022   0.001   TYR A  99 
 ARG   0.004   0.000   ARG B 362 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12888 (  671)
  hydrogen bonds       : angle       5.33600 ( 1938)
  covalent geometry    : bond        0.00289 (13328)
  covalent geometry    : angle       0.60539 (17993)

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

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

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 1.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  915 MET cc_start: 0.7553 (mmt) cc_final: 0.7303 (mmt)
REVERT: A  920 MET cc_start: 0.7535 (tpt) cc_final: 0.6971 (tpp)
REVERT: B  455 LYS cc_start: 0.7618 (tttp) cc_final: 0.7347 (ttmm)
REVERT: B 1001 MET cc_start: 0.3273 (mmm) cc_final: 0.2241 (tpp)
  outliers start: 1
  outliers final: 1
  residues processed: 143
  average time/residue: 0.2538
  time to fit residues: 53.4142
Evaluate side-chains
  137 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 1.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 141 optimal weight:    7.9990
   chunk 126 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 43 optimal weight:    0.1980
   chunk 85 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 130 optimal weight:    6.9990
   chunk 50 optimal weight:    5.9990
   chunk 79 optimal weight:   30.0000
   chunk 97 optimal weight:    7.9990
   chunk 151 optimal weight:    2.9990
   overall best weight:    2.8388

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

Flipped N/Q/H residues before XYZ refinement:
A  75 GLN
A 172 HIS
A 757 GLN
A 873 GLN
A 884 HIS
A 941 GLN
A1013 GLN
A1059 HIS
B  75 GLN
B 826 ASN
B 873 GLN
B 880 GLN
B 884 HIS
B 980 GLN
B1013 GLN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.199072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.175162 restraints weight = 16853.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.169903 restraints weight = 28304.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.168609 restraints weight = 33822.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.4025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.1090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  13328  Z= 0.194
  Angle     :  0.590   6.923  17993  Z= 0.306
  Chirality :  0.041   0.158   2071
  Planarity :  0.004   0.049   2293
  Dihedral  :  4.373  55.506   1782
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 14.85 %
    Favored  : 82.32 %
  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:  0.63 (0.21), residues: 1651
  helix:  1.89 (0.20), residues: 685
  sheet:  0.25 (0.28), residues: 370
  loop : -1.24 (0.25), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 778 
 HIS   0.008   0.001   HIS A 172 
 PHE   0.022   0.002   PHE A 869 
 TYR   0.030   0.002   TYR B 242 
 ARG   0.005   0.000   ARG A1011 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05117 (  671)
  hydrogen bonds       : angle       4.69928 ( 1938)
  covalent geometry    : bond        0.00463 (13328)
  covalent geometry    : angle       0.58958 (17993)

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

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

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 143
  time to evaluate  : 1.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 THR cc_start: 0.7529 (p) cc_final: 0.7304 (m)
REVERT: A  157 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8680 (tt)
REVERT: B  518 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6700 (ptt)
REVERT: B  983 MET cc_start: 0.5527 (tpp) cc_final: 0.5095 (tmm)
REVERT: B 1001 MET cc_start: 0.2684 (mmm) cc_final: 0.1888 (tpp)
  outliers start: 41
  outliers final: 24
  residues processed: 174
  average time/residue: 0.2355
  time to fit residues: 61.5522
Evaluate side-chains
  166 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 140
  time to evaluate  : 1.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  506 CYS
Chi-restraints excluded: chain A residue  756 ILE
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue 1096 MET
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  385 TYR
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  445 CYS
Chi-restraints excluded: chain B residue  518 MET
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  786 THR
Chi-restraints excluded: chain B residue  855 VAL
Chi-restraints excluded: chain B residue  870 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 10 optimal weight:    5.9990
   chunk 82 optimal weight:   30.0000
   chunk 120 optimal weight:    9.9990
   chunk 166 optimal weight:   20.0000
   chunk 2 optimal weight:    2.9990
   chunk 88 optimal weight:   10.0000
   chunk 157 optimal weight:    8.9990
   chunk 17 optimal weight:    9.9990
   chunk 67 optimal weight:   10.0000
   chunk 100 optimal weight:    0.8980
   overall best weight:    3.9386

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

Flipped N/Q/H residues before XYZ refinement:
A1059 HIS
B 142 GLN
B 412 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.195010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.171634 restraints weight = 17059.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.169405 restraints weight = 27762.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.168429 restraints weight = 31448.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.1793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  13328  Z= 0.252
  Angle     :  0.659   8.064  17993  Z= 0.344
  Chirality :  0.043   0.194   2071
  Planarity :  0.005   0.050   2293
  Dihedral  :  4.878  52.038   1782
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 15.88 %
    Favored  : 79.70 %
  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:  0.11 (0.21), residues: 1651
  helix:  1.49 (0.19), residues: 684
  sheet: -0.00 (0.28), residues: 376
  loop : -1.58 (0.25), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 778 
 HIS   0.009   0.001   HIS A 397 
 PHE   0.025   0.002   PHE A 869 
 TYR   0.036   0.002   TYR B 242 
 ARG   0.003   0.000   ARG B 523 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05859 (  671)
  hydrogen bonds       : angle       4.94065 ( 1938)
  covalent geometry    : bond        0.00611 (13328)
  covalent geometry    : angle       0.65924 (17993)

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

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

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 151
  time to evaluate  : 1.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 MET cc_start: 0.7204 (tmm) cc_final: 0.6813 (tmm)
REVERT: A  157 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8710 (tt)
REVERT: A  385 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.8329 (t80)
REVERT: B  518 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6885 (ptt)
REVERT: B  572 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6976 (mt-10)
REVERT: B  807 LYS cc_start: 0.8214 (tmtt) cc_final: 0.7983 (tmtt)
REVERT: B 1001 MET cc_start: 0.2464 (mmm) cc_final: 0.1793 (mtp)
  outliers start: 64
  outliers final: 40
  residues processed: 204
  average time/residue: 0.2270
  time to fit residues: 69.9397
Evaluate side-chains
  175 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 131
  time to evaluate  : 1.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  172 HIS
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  506 CYS
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  756 ILE
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue  851 CYS
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue 1020 MET
Chi-restraints excluded: chain A residue 1096 MET
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  385 TYR
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  409 VAL
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  445 CYS
Chi-restraints excluded: chain B residue  488 ASP
Chi-restraints excluded: chain B residue  518 MET
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  572 GLU
Chi-restraints excluded: chain B residue  786 THR
Chi-restraints excluded: chain B residue  797 MET
Chi-restraints excluded: chain B residue  824 VAL
Chi-restraints excluded: chain B residue  855 VAL
Chi-restraints excluded: chain B residue  870 CYS
Chi-restraints excluded: chain B residue 1059 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 123 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 150 optimal weight:   20.0000
   chunk 114 optimal weight:    0.7980
   chunk 74 optimal weight:   20.0000
   chunk 82 optimal weight:   20.0000
   chunk 36 optimal weight:    0.9990
   chunk 127 optimal weight:    6.9990
   chunk 156 optimal weight:    7.9990
   chunk 135 optimal weight:    0.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A1013 GLN
A1059 HIS
B 142 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.199278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.175694 restraints weight = 16816.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.172364 restraints weight = 27813.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.170568 restraints weight = 35058.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.4048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.1796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13328  Z= 0.131
  Angle     :  0.547   7.826  17993  Z= 0.281
  Chirality :  0.039   0.151   2071
  Planarity :  0.004   0.050   2293
  Dihedral  :  4.406  52.535   1782
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 18.85 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.21), residues: 1651
  helix:  1.88 (0.20), residues: 687
  sheet:  0.11 (0.29), residues: 363
  loop : -1.43 (0.24), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 366 
 HIS   0.004   0.001   HIS B 249 
 PHE   0.018   0.001   PHE A 869 
 TYR   0.021   0.001   TYR B 242 
 ARG   0.003   0.000   ARG A 932 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04251 (  671)
  hydrogen bonds       : angle       4.51529 ( 1938)
  covalent geometry    : bond        0.00301 (13328)
  covalent geometry    : angle       0.54715 (17993)

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

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

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 155
  time to evaluate  : 1.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 MET cc_start: 0.7152 (tmm) cc_final: 0.6927 (tmm)
REVERT: A  157 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8574 (tt)
REVERT: A  313 CYS cc_start: 0.7822 (p) cc_final: 0.7614 (p)
REVERT: B  518 MET cc_start: 0.7201 (ppp) cc_final: 0.6905 (ptt)
REVERT: B 1001 MET cc_start: 0.2162 (mmm) cc_final: 0.1485 (mtp)
  outliers start: 44
  outliers final: 32
  residues processed: 186
  average time/residue: 0.2467
  time to fit residues: 69.2200
Evaluate side-chains
  174 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 141
  time to evaluate  : 1.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  172 HIS
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  441 ASP
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  506 CYS
Chi-restraints excluded: chain A residue  756 ILE
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue 1020 MET
Chi-restraints excluded: chain A residue 1096 MET
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  249 HIS
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  385 TYR
Chi-restraints excluded: chain B residue  409 VAL
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  445 CYS
Chi-restraints excluded: chain B residue  488 ASP
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  797 MET
Chi-restraints excluded: chain B residue  855 VAL
Chi-restraints excluded: chain B residue  870 CYS
Chi-restraints excluded: chain B residue 1059 HIS
Chi-restraints excluded: chain B residue 1072 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 111 optimal weight:    4.9990
   chunk 117 optimal weight:    0.1980
   chunk 101 optimal weight:    9.9990
   chunk 58 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 124 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   chunk 166 optimal weight:    5.9990
   chunk 118 optimal weight:    1.9990
   chunk 145 optimal weight:    1.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 884 HIS
A1059 HIS
** B1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.200135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.176547 restraints weight = 16923.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.171447 restraints weight = 27449.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.170490 restraints weight = 35161.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7236
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  13328  Z= 0.123
  Angle     :  0.544   8.714  17993  Z= 0.276
  Chirality :  0.039   0.130   2071
  Planarity :  0.004   0.051   2293
  Dihedral  :  4.237  53.280   1782
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 19.06 %
    Favored  : 77.14 %
  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:  0.61 (0.21), residues: 1651
  helix:  2.02 (0.20), residues: 688
  sheet:  0.14 (0.29), residues: 366
  loop : -1.38 (0.24), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 366 
 HIS   0.004   0.001   HIS B 249 
 PHE   0.018   0.001   PHE A 869 
 TYR   0.020   0.001   TYR B 242 
 ARG   0.002   0.000   ARG A 299 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04012 (  671)
  hydrogen bonds       : angle       4.38704 ( 1938)
  covalent geometry    : bond        0.00286 (13328)
  covalent geometry    : angle       0.54424 (17993)

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

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

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 155
  time to evaluate  : 1.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 MET cc_start: 0.7115 (tmm) cc_final: 0.6833 (tmm)
REVERT: A  157 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8565 (tt)
REVERT: A  313 CYS cc_start: 0.7912 (p) cc_final: 0.7657 (p)
REVERT: A 1001 MET cc_start: 0.3252 (tpt) cc_final: 0.2813 (tpt)
REVERT: B  408 MET cc_start: 0.7521 (tmm) cc_final: 0.7186 (ttp)
REVERT: B 1001 MET cc_start: 0.2320 (mmm) cc_final: 0.1589 (mtp)
  outliers start: 55
  outliers final: 32
  residues processed: 193
  average time/residue: 0.2314
  time to fit residues: 66.5101
Evaluate side-chains
  173 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 140
  time to evaluate  : 1.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  172 HIS
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  506 CYS
Chi-restraints excluded: chain A residue  756 ILE
Chi-restraints excluded: chain A residue  793 VAL
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue  835 GLU
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue 1020 MET
Chi-restraints excluded: chain A residue 1096 MET
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  249 HIS
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  385 TYR
Chi-restraints excluded: chain B residue  409 VAL
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  488 ASP
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  797 MET
Chi-restraints excluded: chain B residue  870 CYS
Chi-restraints excluded: chain B residue 1059 HIS
Chi-restraints excluded: chain B residue 1072 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 160 optimal weight:   30.0000
   chunk 63 optimal weight:   10.0000
   chunk 50 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 158 optimal weight:   20.0000
   chunk 154 optimal weight:    7.9990
   chunk 35 optimal weight:    9.9990
   chunk 142 optimal weight:    3.9990
   chunk 118 optimal weight:    0.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 884 HIS
A1059 HIS
B1014 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.195895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.173936 restraints weight = 17284.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.171386 restraints weight = 27185.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.169563 restraints weight = 29314.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.4041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  13328  Z= 0.212
  Angle     :  0.647   8.920  17993  Z= 0.327
  Chirality :  0.042   0.171   2071
  Planarity :  0.004   0.052   2293
  Dihedral  :  4.599  53.252   1782
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 18.92 %
    Favored  : 76.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.21), residues: 1651
  helix:  1.77 (0.20), residues: 681
  sheet:  0.05 (0.28), residues: 373
  loop : -1.59 (0.24), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 568 
 HIS   0.006   0.001   HIS A 397 
 PHE   0.023   0.002   PHE A 869 
 TYR   0.031   0.002   TYR B 242 
 ARG   0.009   0.000   ARG A1011 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05204 (  671)
  hydrogen bonds       : angle       4.65787 ( 1938)
  covalent geometry    : bond        0.00515 (13328)
  covalent geometry    : angle       0.64749 (17993)

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

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

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 146
  time to evaluate  : 1.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8684 (tt)
REVERT: A  749 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6713 (tt0)
REVERT: B  416 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8111 (m)
REVERT: B 1001 MET cc_start: 0.2396 (mmm) cc_final: 0.1706 (mtp)
  outliers start: 61
  outliers final: 48
  residues processed: 194
  average time/residue: 0.2363
  time to fit residues: 68.6396
Evaluate side-chains
  189 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 138
  time to evaluate  : 1.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  172 HIS
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  283 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  339 MET
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  506 CYS
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  749 GLU
Chi-restraints excluded: chain A residue  756 ILE
Chi-restraints excluded: chain A residue  793 VAL
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue  835 GLU
Chi-restraints excluded: chain A residue  851 CYS
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  870 CYS
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  881 GLN
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue 1020 MET
Chi-restraints excluded: chain A residue 1059 HIS
Chi-restraints excluded: chain A residue 1096 MET
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  385 TYR
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  409 VAL
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  445 CYS
Chi-restraints excluded: chain B residue  488 ASP
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  786 THR
Chi-restraints excluded: chain B residue  797 MET
Chi-restraints excluded: chain B residue  824 VAL
Chi-restraints excluded: chain B residue  870 CYS
Chi-restraints excluded: chain B residue  933 ILE
Chi-restraints excluded: chain B residue 1059 HIS
Chi-restraints excluded: chain B residue 1072 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 132 optimal weight:    4.9990
   chunk 87 optimal weight:    0.0270
   chunk 140 optimal weight:    2.9990
   chunk 150 optimal weight:    8.9990
   chunk 1 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 148 optimal weight:    3.9990
   chunk 143 optimal weight:    0.8980
   chunk 144 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 145 optimal weight:    4.9990
   overall best weight:    1.7844

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

Flipped N/Q/H residues before XYZ refinement:
A 884 HIS
A1059 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.198314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.175082 restraints weight = 17053.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.171617 restraints weight = 27974.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.170380 restraints weight = 32498.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.4047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13328  Z= 0.142
  Angle     :  0.595   9.068  17993  Z= 0.298
  Chirality :  0.040   0.185   2071
  Planarity :  0.004   0.055   2293
  Dihedral  :  4.419  53.155   1782
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 19.54 %
    Favored  : 76.59 %
  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:  0.41 (0.21), residues: 1651
  helix:  1.89 (0.20), residues: 686
  sheet:  0.07 (0.28), residues: 373
  loop : -1.56 (0.24), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 568 
 HIS   0.004   0.001   HIS A1059 
 PHE   0.022   0.002   PHE B 231 
 TYR   0.023   0.002   TYR B 242 
 ARG   0.006   0.000   ARG A1011 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04337 (  671)
  hydrogen bonds       : angle       4.49422 ( 1938)
  covalent geometry    : bond        0.00335 (13328)
  covalent geometry    : angle       0.59479 (17993)

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

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

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 146
  time to evaluate  : 1.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 MET cc_start: 0.6925 (tmm) cc_final: 0.6712 (tmm)
REVERT: A  157 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8591 (tt)
REVERT: A  749 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6615 (tt0)
REVERT: B 1001 MET cc_start: 0.2457 (mmm) cc_final: 0.1660 (mtp)
  outliers start: 56
  outliers final: 46
  residues processed: 186
  average time/residue: 0.2280
  time to fit residues: 64.1301
Evaluate side-chains
  185 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 137
  time to evaluate  : 1.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  172 HIS
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  283 MET
Chi-restraints excluded: chain A residue  339 MET
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  506 CYS
Chi-restraints excluded: chain A residue  749 GLU
Chi-restraints excluded: chain A residue  756 ILE
Chi-restraints excluded: chain A residue  793 VAL
Chi-restraints excluded: chain A residue  829 VAL
Chi-restraints excluded: chain A residue  835 GLU
Chi-restraints excluded: chain A residue  851 CYS
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  870 CYS
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  881 GLN
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  965 MET
Chi-restraints excluded: chain A residue 1020 MET
Chi-restraints excluded: chain A residue 1096 MET
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  339 MET
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  385 TYR
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  409 VAL
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  445 CYS
Chi-restraints excluded: chain B residue  488 ASP
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  745 PHE
Chi-restraints excluded: chain B residue  746 THR
Chi-restraints excluded: chain B residue  797 MET
Chi-restraints excluded: chain B residue  855 VAL
Chi-restraints excluded: chain B residue  870 CYS
Chi-restraints excluded: chain B residue 1059 HIS
Chi-restraints excluded: chain B residue 1072 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 138 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 82 optimal weight:   10.0000
   chunk 55 optimal weight:    0.3980
   chunk 159 optimal weight:   20.0000
   chunk 67 optimal weight:    7.9990
   chunk 129 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0670
   chunk 154 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 128 optimal weight:    0.9980
   overall best weight:    0.8922

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

Flipped N/Q/H residues before XYZ refinement:
A 884 HIS
A1059 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.201329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.178121 restraints weight = 17195.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.176450 restraints weight = 27159.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.175717 restraints weight = 26905.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.4108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  13328  Z= 0.110
  Angle     :  0.562   8.725  17993  Z= 0.279
  Chirality :  0.039   0.142   2071
  Planarity :  0.004   0.054   2293
  Dihedral  :  4.131  53.726   1782
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 20.44 %
    Favored  : 76.45 %
  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:  0.65 (0.21), residues: 1651
  helix:  2.11 (0.20), residues: 685
  sheet:  0.18 (0.29), residues: 356
  loop : -1.42 (0.24), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 568 
 HIS   0.003   0.001   HIS A1059 
 PHE   0.017   0.001   PHE B 231 
 TYR   0.017   0.001   TYR B 242 
 ARG   0.004   0.000   ARG A1011 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03555 (  671)
  hydrogen bonds       : angle       4.27571 ( 1938)
  covalent geometry    : bond        0.00249 (13328)
  covalent geometry    : angle       0.56184 (17993)

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

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

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 143
  time to evaluate  : 1.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8545 (tt)
REVERT: A  226 MET cc_start: 0.8197 (tpt) cc_final: 0.7918 (tpt)
REVERT: A  280 PHE cc_start: 0.7262 (t80) cc_final: 0.7028 (t80)
REVERT: B  807 LYS cc_start: 0.7641 (tmtt) cc_final: 0.7427 (tmtt)
REVERT: B 1001 MET cc_start: 0.2281 (mmm) cc_final: 0.1505 (mtp)
  outliers start: 45
  outliers final: 35
  residues processed: 175
  average time/residue: 0.2353
  time to fit residues: 61.8871
Evaluate side-chains
  170 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 134
  time to evaluate  : 1.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  172 HIS
Chi-restraints excluded: chain A residue  283 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  397 HIS
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  441 ASP
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  506 CYS
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  518 MET
Chi-restraints excluded: chain A residue  756 ILE
Chi-restraints excluded: chain A residue  835 GLU
Chi-restraints excluded: chain A residue  851 CYS
Chi-restraints excluded: chain A residue  870 CYS
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  881 GLN
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  965 MET
Chi-restraints excluded: chain A residue 1020 MET
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  385 TYR
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  445 CYS
Chi-restraints excluded: chain B residue  746 THR
Chi-restraints excluded: chain B residue  797 MET
Chi-restraints excluded: chain B residue  870 CYS
Chi-restraints excluded: chain B residue 1059 HIS
Chi-restraints excluded: chain B residue 1068 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 43 optimal weight:    0.0980
   chunk 50 optimal weight:    4.9990
   chunk 107 optimal weight:    9.9990
   chunk 76 optimal weight:   10.0000
   chunk 54 optimal weight:    7.9990
   chunk 99 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 90 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   chunk 154 optimal weight:    3.9990
   chunk 136 optimal weight:    3.9990
   overall best weight:    2.8188

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

Flipped N/Q/H residues before XYZ refinement:
A 884 HIS
A1059 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.196425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.172743 restraints weight = 17011.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.168893 restraints weight = 28526.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.167878 restraints weight = 35351.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.4024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.2430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073  13328  Z= 0.193
  Angle     :  0.648  10.804  17993  Z= 0.324
  Chirality :  0.042   0.340   2071
  Planarity :  0.004   0.053   2293
  Dihedral  :  4.468  53.737   1782
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.10 %
    Favored  : 76.10 %
  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:  0.37 (0.21), residues: 1651
  helix:  1.86 (0.20), residues: 680
  sheet:  0.11 (0.28), residues: 371
  loop : -1.60 (0.24), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 366 
 HIS   0.006   0.001   HIS A 397 
 PHE   0.021   0.002   PHE A 869 
 TYR   0.028   0.002   TYR B 242 
 ARG   0.006   0.000   ARG A1011 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04915 (  671)
  hydrogen bonds       : angle       4.57899 ( 1938)
  covalent geometry    : bond        0.00470 (13328)
  covalent geometry    : angle       0.64832 (17993)

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

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

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 138
  time to evaluate  : 1.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8667 (tt)
REVERT: A  264 TYR cc_start: 0.6660 (m-10) cc_final: 0.6417 (m-10)
REVERT: A  280 PHE cc_start: 0.7313 (t80) cc_final: 0.7027 (t80)
REVERT: A  425 MET cc_start: 0.8314 (mmt) cc_final: 0.8095 (mmm)
REVERT: A 1096 MET cc_start: 0.3064 (OUTLIER) cc_final: 0.2594 (mmt)
REVERT: B  807 LYS cc_start: 0.7838 (tmtt) cc_final: 0.7637 (tmtt)
REVERT: B 1001 MET cc_start: 0.2429 (mmm) cc_final: 0.1643 (mtp)
  outliers start: 55
  outliers final: 46
  residues processed: 177
  average time/residue: 0.2209
  time to fit residues: 59.5324
Evaluate side-chains
  179 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 131
  time to evaluate  : 1.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  172 HIS
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  283 MET
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  441 ASP
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  506 CYS
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  518 MET
Chi-restraints excluded: chain A residue  756 ILE
Chi-restraints excluded: chain A residue  835 GLU
Chi-restraints excluded: chain A residue  851 CYS
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  870 CYS
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  881 GLN
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  965 MET
Chi-restraints excluded: chain A residue 1020 MET
Chi-restraints excluded: chain A residue 1096 MET
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  339 MET
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  385 TYR
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  445 CYS
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  746 THR
Chi-restraints excluded: chain B residue  786 THR
Chi-restraints excluded: chain B residue  797 MET
Chi-restraints excluded: chain B residue  829 VAL
Chi-restraints excluded: chain B residue  870 CYS
Chi-restraints excluded: chain B residue  933 ILE
Chi-restraints excluded: chain B residue 1059 HIS
Chi-restraints excluded: chain B residue 1072 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 33 optimal weight:    0.0020
   chunk 69 optimal weight:    0.8980
   chunk 116 optimal weight:    0.6980
   chunk 160 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 111 optimal weight:    0.7980
   chunk 134 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 40 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.6588

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

Flipped N/Q/H residues before XYZ refinement:
A 884 HIS
A1059 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.202282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.179546 restraints weight = 17131.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.176259 restraints weight = 29242.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.175261 restraints weight = 33167.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.4099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7125
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  13328  Z= 0.109
  Angle     :  0.593  11.740  17993  Z= 0.291
  Chirality :  0.039   0.143   2071
  Planarity :  0.004   0.054   2293
  Dihedral  :  4.125  53.536   1782
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 21.55 %
    Favored  : 76.17 %
  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:  0.67 (0.21), residues: 1651
  helix:  2.12 (0.20), residues: 685
  sheet:  0.15 (0.29), residues: 350
  loop : -1.36 (0.24), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 568 
 HIS   0.005   0.001   HIS B 525 
 PHE   0.015   0.001   PHE B1067 
 TYR   0.016   0.001   TYR B 242 
 ARG   0.003   0.000   ARG B 564 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03429 (  671)
  hydrogen bonds       : angle       4.24070 ( 1938)
  covalent geometry    : bond        0.00243 (13328)
  covalent geometry    : angle       0.59336 (17993)

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

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

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 140
  time to evaluate  : 1.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  226 MET cc_start: 0.8205 (tpt) cc_final: 0.7978 (tpt)
REVERT: A  280 PHE cc_start: 0.7300 (t80) cc_final: 0.7034 (t80)
REVERT: B  283 MET cc_start: 0.7450 (ttm) cc_final: 0.7178 (mtt)
REVERT: B  408 MET cc_start: 0.7345 (tmm) cc_final: 0.7023 (ttp)
REVERT: B 1001 MET cc_start: 0.2306 (mmm) cc_final: 0.1789 (mtp)
  outliers start: 33
  outliers final: 29
  residues processed: 164
  average time/residue: 0.2430
  time to fit residues: 59.4370
Evaluate side-chains
  161 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 132
  time to evaluate  : 1.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  172 HIS
Chi-restraints excluded: chain A residue  283 MET
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  397 HIS
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  441 ASP
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  506 CYS
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  835 GLU
Chi-restraints excluded: chain A residue  851 CYS
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  870 CYS
Chi-restraints excluded: chain A residue  881 GLN
Chi-restraints excluded: chain A residue  965 MET
Chi-restraints excluded: chain A residue 1020 MET
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  385 TYR
Chi-restraints excluded: chain B residue  445 CYS
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  746 THR
Chi-restraints excluded: chain B residue  797 MET
Chi-restraints excluded: chain B residue  870 CYS
Chi-restraints excluded: chain B residue 1059 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 145 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0020
   chunk 54 optimal weight:    1.9990
   chunk 119 optimal weight:    6.9990
   chunk 101 optimal weight:    7.9990
   chunk 87 optimal weight:    0.8980
   chunk 95 optimal weight:    7.9990
   chunk 126 optimal weight:    0.9990
   chunk 88 optimal weight:    0.0040
   chunk 157 optimal weight:    8.9990
   overall best weight:    0.7804

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

Flipped N/Q/H residues before XYZ refinement:
A 884 HIS
A1059 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.202326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.179831 restraints weight = 17133.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.178452 restraints weight = 29182.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.176542 restraints weight = 30151.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.4114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.2458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  13328  Z= 0.111
  Angle     :  0.596  11.199  17993  Z= 0.292
  Chirality :  0.039   0.145   2071
  Planarity :  0.004   0.053   2293
  Dihedral  :  4.024  54.578   1782
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 22.10 %
    Favored  : 75.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.21), residues: 1651
  helix:  2.23 (0.20), residues: 685
  sheet:  0.20 (0.29), residues: 351
  loop : -1.27 (0.24), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 521 
 HIS   0.003   0.001   HIS B 249 
 PHE   0.016   0.001   PHE A 869 
 TYR   0.016   0.001   TYR B 242 
 ARG   0.003   0.000   ARG A 299 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03443 (  671)
  hydrogen bonds       : angle       4.15353 ( 1938)
  covalent geometry    : bond        0.00253 (13328)
  covalent geometry    : angle       0.59553 (17993)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3607.06 seconds
wall clock time: 64 minutes 8.36 seconds (3848.36 seconds total)