Starting phenix.real_space_refine
on Thu Feb 13 04:27:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bv1_30209/02_2025/7bv1_30209.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bv1_30209/02_2025/7bv1_30209.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7bv1_30209/02_2025/7bv1_30209.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bv1_30209/02_2025/7bv1_30209.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bv1_30209/02_2025/7bv1_30209.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bv1_30209/02_2025/7bv1_30209.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      64      5.16       5
     C    5626      2.51       5
     N    1460      2.21       5
     O    1647      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8799
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 6724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 836, 6724
          Classifications: {'peptide': 836}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 807}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 14
    Chain: "B"
      Number of atoms: 865
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 865
          Classifications: {'peptide': 114}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "C"
      Number of atoms: 481
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 481
          Classifications: {'peptide': 63}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 62}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "D"
      Number of atoms: 727
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 727
          Classifications: {'peptide': 99}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 5, 'TRANS': 93}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 25
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1825  SG  CYS A 301      40.360  63.172  37.957  1.00 10.69           S
  ATOM   1866  SG  CYS A 306      40.337  62.023  34.421  1.00  7.82           S
  ATOM   1898  SG  CYS A 310      43.496  61.958  36.510  1.00 18.90           S
  ATOM   3300  SG  CYS A 487      23.293  58.642  47.127  1.00 13.60           S
  ATOM   4553  SG  CYS A 645      21.979  58.294  43.851  1.00 17.07           S
  ATOM   4559  SG  CYS A 646      25.396  60.467  44.225  1.00 15.31           S

  Time building chain proxies: 5.13, per 1000 atoms: 0.58
  Number of scatterers: 8799
  At special positions: 0
  Unit cell: (90.246, 93.288, 127.764, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      64     16.00
     O    1647      8.00
     N    1460      7.00
     C    5626      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: 2.31
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1001 "
        pdb="ZN    ZN A1001 " - pdb=" ND1 HIS A 295 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 310 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 301 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 306 "
      pdb="  ZN A1002 "
        pdb="ZN    ZN A1002 " - pdb=" ND1 HIS A 642 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 645 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 487 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 646 "
      Number of angles added : 6


  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2134

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 11 sheets defined
      50.5% alpha, 16.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 84 through 90
      removed outlier: 3.964A  pdb=" N   TYR A  87 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 133
    Processing helix  chain 'A' and resid 139 through 149
    Processing helix  chain 'A' and resid 153 through 159
      removed outlier: 3.620A  pdb=" N   PHE A 157 " --> pdb=" O   ASP A 154 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LYS A 159 " --> pdb=" O   TYR A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 177
    Processing helix  chain 'A' and resid 178 through 200
      removed outlier: 3.630A  pdb=" N   ALA A 185 " --> pdb=" O   ARG A 181 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU A 186 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 210
    Processing helix  chain 'A' and resid 234 through 242
    Processing helix  chain 'A' and resid 242 through 248
      removed outlier: 4.351A  pdb=" N   THR A 246 " --> pdb=" O   MET A 242 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   LEU A 247 " --> pdb=" O   PRO A 243 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   THR A 248 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 242 through 248'
    Processing helix  chain 'A' and resid 249 through 256
      removed outlier: 3.671A  pdb=" N   THR A 252 " --> pdb=" O   ARG A 249 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   ALA A 253 " --> pdb=" O   ALA A 250 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   HIS A 256 " --> pdb=" O   ALA A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 287
    Processing helix  chain 'A' and resid 297 through 301
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.611A  pdb=" N   LEU A 316 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 326
      removed outlier: 3.820A  pdb=" N   PHE A 326 " --> pdb=" O   PRO A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 375
    Processing helix  chain 'A' and resid 377 through 385
      removed outlier: 4.702A  pdb=" N   HIS A 381 " --> pdb=" O   ASP A 377 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALA A 383 " --> pdb=" O   ALA A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 426
      removed outlier: 3.651A  pdb=" N   TYR A 420 " --> pdb=" O   ASN A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 454
    Processing helix  chain 'A' and resid 455 through 459
      removed outlier: 3.528A  pdb=" N   TYR A 458 " --> pdb=" O   TYR A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 480
      removed outlier: 3.796A  pdb=" N   GLU A 474 " --> pdb=" O   LEU A 470 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASP A 477 " --> pdb=" O   VAL A 473 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   LYS A 478 " --> pdb=" O   GLU A 474 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   TYR A 479 " --> pdb=" O   VAL A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 519
      removed outlier: 3.954A  pdb=" N   TYR A 515 " --> pdb=" O   LYS A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 534
    Processing helix  chain 'A' and resid 561 through 580
      removed outlier: 4.343A  pdb=" N   THR A 567 " --> pdb=" O   CYS A 563 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   LYS A 574 " --> pdb=" O   GLN A 570 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   LEU A 575 " --> pdb=" O   PHE A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 607
    Processing helix  chain 'A' and resid 621 through 626
    Processing helix  chain 'A' and resid 627 through 639
    Processing helix  chain 'A' and resid 647 through 663
    Processing helix  chain 'A' and resid 686 through 709
      removed outlier: 3.635A  pdb=" N   ALA A 690 " --> pdb=" O   THR A 686 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 717 through 733
      removed outlier: 3.765A  pdb=" N   ARG A 721 " --> pdb=" O   ASP A 717 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   ASN A 722 " --> pdb=" O   LYS A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 752
    Processing helix  chain 'A' and resid 768 through 772
    Processing helix  chain 'A' and resid 778 through 791
      removed outlier: 3.820A  pdb=" N   PHE A 782 " --> pdb=" O   SER A 778 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ASN A 791 " --> pdb=" O   TYR A 787 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 833 through 842
    Processing helix  chain 'A' and resid 852 through 867
      removed outlier: 3.683A  pdb=" N   ILE A 856 " --> pdb=" O   GLY A 852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 868 through 872
    Processing helix  chain 'A' and resid 874 through 895
      removed outlier: 3.588A  pdb=" N   VAL A 880 " --> pdb=" O   GLU A 876 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   PHE A 881 " --> pdb=" O   TYR A 877 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   HIS A 882 " --> pdb=" O   ALA A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 918 through 923
    Processing helix  chain 'A' and resid 924 through 926
      No H-bonds generated for 'chain 'A' and resid 924 through 926'
    Processing helix  chain 'B' and resid 79 through 97
      removed outlier: 3.626A  pdb=" N   ARG B  96 " --> pdb=" O   PHE B  92 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   LYS B  97 " --> pdb=" O   THR B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 108
      removed outlier: 3.920A  pdb=" N   ASN B 105 " --> pdb=" O   ASP B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 114
      removed outlier: 3.740A  pdb=" N   CYS B 114 " --> pdb=" O   ARG B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 125
    Processing helix  chain 'B' and resid 134 through 142
      removed outlier: 3.662A  pdb=" N   ASN B 140 " --> pdb=" O   ASN B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 180
    Processing helix  chain 'C' and resid 3 through 20
      removed outlier: 3.579A  pdb=" N   LYS C   7 " --> pdb=" O   MET C   3 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   VAL C  11 " --> pdb=" O   LYS C   7 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   VAL C  12 " --> pdb=" O   CYS C   8 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 25
    Processing helix  chain 'C' and resid 26 through 40
      removed outlier: 3.816A  pdb=" N   GLN C  31 " --> pdb=" O   LYS C  27 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 61
      removed outlier: 3.805A  pdb=" N   SER C  54 " --> pdb=" O   GLU C  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.922A  pdb=" N   THR D  93 " --> pdb=" O   THR D  89 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   MET D  94 " --> pdb=" O   MET D  90 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   ASP D  99 " --> pdb=" O   LEU D  95 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 112
      removed outlier: 4.344A  pdb=" N   ILE D 106 " --> pdb=" O   ALA D 102 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ASP D 112 " --> pdb=" O   ASN D 108 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 137 through 141
    Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 38
    Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 224
      removed outlier: 3.637A  pdb=" N   GLY A 203 " --> pdb=" O   VAL A 231 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 354
      removed outlier: 3.595A  pdb=" N   VAL A 338 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   LEU A 329 " --> pdb=" O   THR A 344 " (cutoff:3.500A)
      removed outlier: 5.070A  pdb=" N   TYR A 346 " --> pdb=" O   GLY A 327 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   GLY A 327 " --> pdb=" O   TYR A 346 " (cutoff:3.500A)
      removed outlier: 9.268A  pdb=" N   SER A 363 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   PHE A 334 " --> pdb=" O   SER A 363 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 354
      removed outlier: 3.595A  pdb=" N   VAL A 338 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   LEU A 329 " --> pdb=" O   THR A 344 " (cutoff:3.500A)
      removed outlier: 5.070A  pdb=" N   TYR A 346 " --> pdb=" O   GLY A 327 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   GLY A 327 " --> pdb=" O   TYR A 346 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 556 through 559
      removed outlier: 7.007A  pdb=" N   THR A 540 " --> pdb=" O   MET A 668 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ALA A 399 " --> pdb=" O   LEU A 673 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   VAL A 675 " --> pdb=" O   SER A 397 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   SER A 397 " --> pdb=" O   VAL A 675 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   VAL A 398 " --> pdb=" O   LEU A 388 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   LEU A 388 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   LEU B 189 " --> pdb=" O   ILE B 156 " (cutoff:3.500A)
      removed outlier: 5.768A  pdb=" N   ILE B 156 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559
      removed outlier: 7.007A  pdb=" N   THR A 540 " --> pdb=" O   MET A 668 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ALA A 399 " --> pdb=" O   LEU A 673 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   VAL A 675 " --> pdb=" O   SER A 397 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   SER A 397 " --> pdb=" O   VAL A 675 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   VAL A 398 " --> pdb=" O   LEU A 388 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   LEU A 388 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   LEU B 189 " --> pdb=" O   ILE B 156 " (cutoff:3.500A)
      removed outlier: 5.768A  pdb=" N   ILE B 156 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   VAL B 159 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415
      removed outlier: 3.768A  pdb=" N   ASN A 414 " --> pdb=" O   VAL A 844 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 753 through 757
    Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 822
    Processing sheet with id=AB1, first strand: chain 'D' and resid 131 through 132
    Processing sheet with id=AB2, first strand: chain 'D' and resid 146 through 149
      removed outlier: 3.986A  pdb=" N   GLU D 155 " --> pdb=" O   LEU D 189 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU D 189 " --> pdb=" O   GLU D 155 " (cutoff:3.500A)

    438 hydrogen bonds defined for protein.
    1191 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.03

  Time building geometry restraints manager: 2.64 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: 2798
        1.34 -     1.46: 2134
        1.46 -     1.59: 3963
        1.59 -     1.71: 0
        1.71 -     1.84: 97
  Bond restraints: 8992
  Sorted by residual:
  bond pdb=" N   VAL A 662 "
       pdb=" CA  VAL A 662 "
    ideal  model  delta    sigma   weight residual
    1.457  1.499 -0.043 1.07e-02 8.73e+03 1.60e+01
  bond pdb=" N   LYS A 263 "
       pdb=" CA  LYS A 263 "
    ideal  model  delta    sigma   weight residual
    1.453  1.483 -0.030 8.30e-03 1.45e+04 1.27e+01
  bond pdb=" N   ILE D 166 "
       pdb=" CA  ILE D 166 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.17e-02 7.31e+03 9.14e+00
  bond pdb=" N   ILE A 847 "
       pdb=" CA  ILE A 847 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.89e+00
  bond pdb=" N   VAL A 844 "
       pdb=" CA  VAL A 844 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.035 1.18e-02 7.18e+03 8.85e+00
  ... (remaining 8987 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 11449
        1.60 -     3.20: 666
        3.20 -     4.80: 86
        4.80 -     6.40: 16
        6.40 -     8.00: 5
  Bond angle restraints: 12222
  Sorted by residual:
  angle pdb=" C   PRO D 121 "
        pdb=" CA  PRO D 121 "
        pdb=" CB  PRO D 121 "
      ideal   model   delta    sigma   weight residual
     111.40  107.43    3.97 9.10e-01 1.21e+00 1.90e+01
  angle pdb=" CA  ALA A 660 "
        pdb=" C   ALA A 660 "
        pdb=" O   ALA A 660 "
      ideal   model   delta    sigma   weight residual
     120.82  116.78    4.04 1.05e+00 9.07e-01 1.48e+01
  angle pdb=" CA  ALA D 125 "
        pdb=" C   ALA D 125 "
        pdb=" O   ALA D 125 "
      ideal   model   delta    sigma   weight residual
     122.27  118.08    4.19 1.16e+00 7.43e-01 1.31e+01
  angle pdb=" N   GLN A 661 "
        pdb=" CA  GLN A 661 "
        pdb=" C   GLN A 661 "
      ideal   model   delta    sigma   weight residual
     111.36  115.27   -3.91 1.09e+00 8.42e-01 1.29e+01
  angle pdb=" N   LEU A 401 "
        pdb=" CA  LEU A 401 "
        pdb=" C   LEU A 401 "
      ideal   model   delta    sigma   weight residual
     112.54  116.87   -4.33 1.22e+00 6.72e-01 1.26e+01
  ... (remaining 12217 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.13: 4739
       18.13 -    36.25: 496
       36.25 -    54.38: 87
       54.38 -    72.51: 14
       72.51 -    90.63: 7
  Dihedral angle restraints: 5343
    sinusoidal: 2045
      harmonic: 3298
  Sorted by residual:
  dihedral pdb=" CA  LEU A 758 "
           pdb=" C   LEU A 758 "
           pdb=" N   SER A 759 "
           pdb=" CA  SER A 759 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.32  -26.68     0      5.00e+00 4.00e-02 2.85e+01
  dihedral pdb=" CA  ILE A 757 "
           pdb=" C   ILE A 757 "
           pdb=" N   LEU A 758 "
           pdb=" CA  LEU A 758 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.82   18.18     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" C   ASP A 208 "
           pdb=" N   ASP A 208 "
           pdb=" CA  ASP A 208 "
           pdb=" CB  ASP A 208 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.33    8.73     0      2.50e+00 1.60e-01 1.22e+01
  ... (remaining 5340 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1156
       0.070 -    0.140: 193
       0.140 -    0.210: 32
       0.210 -    0.280: 8
       0.280 -    0.350: 4
  Chirality restraints: 1393
  Sorted by residual:
  chirality pdb=" CA  ASN A 150 "
            pdb=" N   ASN A 150 "
            pdb=" C   ASN A 150 "
            pdb=" CB  ASN A 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.07e+00
  chirality pdb=" CA  ILE D 120 "
            pdb=" N   ILE D 120 "
            pdb=" C   ILE D 120 "
            pdb=" CB  ILE D 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.75   -0.31 2.00e-01 2.50e+01 2.43e+00
  chirality pdb=" CB  ILE A 888 "
            pdb=" CA  ILE A 888 "
            pdb=" CG1 ILE A 888 "
            pdb=" CG2 ILE A 888 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.31 2.00e-01 2.50e+01 2.34e+00
  ... (remaining 1390 not shown)

  Planarity restraints: 1555
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 231 "    0.037 5.00e-02 4.00e+02   5.56e-02 4.95e+00
        pdb=" N   PRO A 232 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A 232 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 232 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 667 "   -0.010 2.00e-02 2.50e+03   2.12e-02 4.49e+00
        pdb=" C   VAL A 667 "    0.037 2.00e-02 2.50e+03
        pdb=" O   VAL A 667 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   MET A 668 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 161 "    0.011 2.00e-02 2.50e+03   2.10e-02 4.43e+00
        pdb=" C   ASP A 161 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   ASP A 161 "    0.014 2.00e-02 2.50e+03
        pdb=" N   TRP A 162 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1552 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 2132
        2.79 -     3.32: 8266
        3.32 -     3.85: 13878
        3.85 -     4.37: 17030
        4.37 -     4.90: 28844
  Nonbonded interactions: 70150
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 194 "
            pdb=" OH  TYR A 289 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O   ASP A 684 "
            pdb=" OG1 THR A 687 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" N   GLU A 136 "
            pdb=" OE1 GLU A 136 "
     model   vdw
     2.380 3.120
  nonbonded pdb=" O   PRO A 322 "
            pdb=" OG  SER A 325 "
     model   vdw
     2.387 3.040
  nonbonded pdb=" OG1 THR A 409 "
            pdb=" OE2 GLU C  23 "
     model   vdw
     2.392 3.040
  ... (remaining 70145 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 'B' and (resid 85 through 95 or (resid 96 through 97 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 98 through 121 or (resid 122 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 123 through 126 or  \ 
(resid 127 and (name N or name CA or name C or name O or name CB )) or resid 128 \ 
 through 133 or (resid 134 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 135 or (resid 136 and (name N or name CA or name C or name O or nam \ 
e CB )) or resid 137 through 138 or (resid 139 and (name N or name CA or name C  \ 
or name O or name CB )) or resid 140 through 169 or resid 176 through 181 or (re \ 
sid 182 and (name N or name CA or name C or name O or name CB )) or resid 183 th \ 
rough 189))
  selection = (chain 'D' and (resid 85 through 96 or (resid 97 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 98 through 189))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             0.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     24.490
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  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:11.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8992  Z= 0.327
  Angle     :  0.816   8.000  12222  Z= 0.527
  Chirality :  0.058   0.350   1393
  Planarity :  0.005   0.056   1555
  Dihedral  : 15.134  90.631   3209
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -1.91 (0.24), residues: 1095
  helix: -0.92 (0.23), residues: 491
  sheet: -1.23 (0.43), residues: 125
  loop : -1.51 (0.26), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 162 
 HIS   0.004   0.001   HIS A 892 
 PHE   0.023   0.002   PHE A 471 
 TYR   0.021   0.002   TYR D 138 
 ARG   0.004   0.001   ARG A 197 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
REVERT: A  334 PHE cc_start: 0.6846 (m-80) cc_final: 0.6589 (m-80)
REVERT: A  760 ASP cc_start: 0.5906 (p0) cc_final: 0.5679 (p0)
  outliers start: 0
  outliers final: 1
  residues processed: 248
  average time/residue: 1.0477
  time to fit residues: 279.9005
Evaluate side-chains
  162 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 161
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  445 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    7.9990
   chunk 82 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0670
   chunk 55 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 85 optimal weight:    9.9990
   chunk 33 optimal weight:    4.9990
   chunk 51 optimal weight:    0.5980
   chunk 63 optimal weight:    9.9990
   chunk 98 optimal weight:   10.0000
   overall best weight:    1.5324

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
A 224 GLN
A 543 ASN
A 703 ASN
A 773 GLN
A 781 ASN
A 790 ASN
A 815 GLN
A 872 HIS
A 886 GLN
A 928 HIS
B 100 ASN
B 176 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.189494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.154941 restraints weight = 10172.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3811 rms_B_bonded: 2.03
r_work: 0.3657 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3545 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.2662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8992  Z= 0.215
  Angle     :  0.595   6.543  12222  Z= 0.319
  Chirality :  0.045   0.170   1393
  Planarity :  0.005   0.073   1555
  Dihedral  :  4.409  20.646   1206
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 15.98 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -1.16 (0.25), residues: 1095
  helix: -0.30 (0.23), residues: 518
  sheet: -1.02 (0.45), residues: 111
  loop : -1.11 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 162 
 HIS   0.007   0.001   HIS A 309 
 PHE   0.020   0.002   PHE A 652 
 TYR   0.016   0.002   TYR A 653 
 ARG   0.004   0.000   ARG B  80 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 173
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
REVERT: A  334 PHE cc_start: 0.7383 (m-80) cc_final: 0.6841 (m-80)
REVERT: A  361 LEU cc_start: 0.7081 (mt) cc_final: 0.6621 (tt)
REVERT: A  415 PHE cc_start: 0.7267 (t80) cc_final: 0.6843 (t80)
REVERT: A  438 LYS cc_start: 0.7095 (mttm) cc_final: 0.6895 (mtpm)
REVERT: A  508 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7874 (mmtp)
REVERT: A  553 ARG cc_start: 0.6061 (mmm-85) cc_final: 0.5387 (mtp85)
REVERT: A  662 VAL cc_start: 0.7945 (m) cc_final: 0.7724 (t)
REVERT: A  750 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7727 (mmp-170)
REVERT: A  760 ASP cc_start: 0.6550 (p0) cc_final: 0.6283 (OUTLIER)
REVERT: A  811 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7428 (mm-30)
REVERT: A  815 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7645 (mp10)
REVERT: B  155 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7500 (pm20)
REVERT: B  176 ASN cc_start: 0.8211 (t0) cc_final: 0.7957 (t0)
REVERT: C    3 MET cc_start: 0.6397 (ttp) cc_final: 0.5632 (tpt)
REVERT: C   43 LYS cc_start: 0.5931 (ptpp) cc_final: 0.5694 (mtmm)
REVERT: C   56 LEU cc_start: 0.7401 (tp) cc_final: 0.7196 (tp)
  outliers start: 36
  outliers final: 14
  residues processed: 189
  average time/residue: 0.9955
  time to fit residues: 203.6447
Evaluate side-chains
  161 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 143
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  208 ASP
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  434 SER
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  508 LYS
Chi-restraints excluded: chain A residue  635 SER
Chi-restraints excluded: chain A residue  643 THR
Chi-restraints excluded: chain A residue  680 THR
Chi-restraints excluded: chain A residue  750 ARG
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain A residue  815 GLN
Chi-restraints excluded: chain A residue  929 THR
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   35 LEU
Chi-restraints excluded: chain C residue   46 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 60 optimal weight:    8.9990
   chunk 20 optimal weight:    0.7980
   chunk 87 optimal weight:    9.9990
   chunk 62 optimal weight:    7.9990
   chunk 96 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   chunk 104 optimal weight:    0.9980
   chunk 67 optimal weight:    5.9990
   chunk 18 optimal weight:    9.9990
   overall best weight:    1.4782

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

Flipped N/Q/H residues before XYZ refinement:
A 224 GLN
A 543 ASN
A 599 HIS
A 872 HIS
B 118 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.187415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.153255 restraints weight = 10384.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 1.82
r_work: 0.3580 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3464 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.3399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8992  Z= 0.190
  Angle     :  0.533   7.984  12222  Z= 0.286
  Chirality :  0.043   0.141   1393
  Planarity :  0.004   0.051   1555
  Dihedral  :  4.191  20.733   1204
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 17.84 %
    Favored  : 78.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -0.99 (0.25), residues: 1095
  helix: -0.05 (0.23), residues: 526
  sheet: -0.94 (0.43), residues: 121
  loop : -1.19 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 916 
 HIS   0.006   0.001   HIS A 309 
 PHE   0.015   0.002   PHE A 652 
 TYR   0.020   0.002   TYR A 867 
 ARG   0.004   0.000   ARG A 392 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 153
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.7891 (mmm) cc_final: 0.7655 (mmt)
REVERT: A  334 PHE cc_start: 0.7506 (m-80) cc_final: 0.6946 (m-80)
REVERT: A  361 LEU cc_start: 0.7255 (mt) cc_final: 0.6708 (tt)
REVERT: A  415 PHE cc_start: 0.7317 (t80) cc_final: 0.6907 (t80)
REVERT: A  508 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.7970 (mmtp)
REVERT: A  553 ARG cc_start: 0.6281 (mmm-85) cc_final: 0.5499 (mtp85)
REVERT: A  750 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7626 (mmp-170)
REVERT: A  760 ASP cc_start: 0.6688 (p0) cc_final: 0.6454 (p0)
REVERT: A  811 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7333 (mm-30)
REVERT: A  815 GLN cc_start: 0.7989 (mt0) cc_final: 0.7781 (mt0)
REVERT: A  826 TYR cc_start: 0.7664 (m-80) cc_final: 0.7396 (m-10)
REVERT: A  926 THR cc_start: 0.8142 (t) cc_final: 0.7930 (m)
REVERT: B  137 THR cc_start: 0.8436 (m) cc_final: 0.8075 (p)
REVERT: B  155 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7498 (pm20)
REVERT: B  176 ASN cc_start: 0.8370 (t0) cc_final: 0.7980 (t160)
REVERT: C    8 CYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7353 (m)
REVERT: C   35 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7231 (mp)
REVERT: C   56 LEU cc_start: 0.7369 (tp) cc_final: 0.7166 (tp)
  outliers start: 34
  outliers final: 17
  residues processed: 176
  average time/residue: 1.0100
  time to fit residues: 192.0604
Evaluate side-chains
  161 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 138
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  208 ASP
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  508 LYS
Chi-restraints excluded: chain A residue  635 SER
Chi-restraints excluded: chain A residue  643 THR
Chi-restraints excluded: chain A residue  680 THR
Chi-restraints excluded: chain A residue  750 ARG
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  778 SER
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain C residue    8 CYS
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   35 LEU
Chi-restraints excluded: chain C residue   46 THR
Chi-restraints excluded: chain D residue  124 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 46 optimal weight:    8.9990
   chunk 63 optimal weight:    8.9990
   chunk 95 optimal weight:   10.0000
   chunk 90 optimal weight:    9.9990
   chunk 10 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 99 optimal weight:    5.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 224 GLN
A 543 ASN
A 573 GLN
A 752 HIS
A 815 GLN
** A 872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 118 ASN
B 140 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.182540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.148841 restraints weight = 10252.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 1.91
r_work: 0.3519 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3400 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.4613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   8992  Z= 0.358
  Angle     :  0.645   9.955  12222  Z= 0.342
  Chirality :  0.047   0.149   1393
  Planarity :  0.005   0.042   1555
  Dihedral  :  4.752  23.350   1204
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 19.19 %
    Favored  : 75.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -1.27 (0.24), residues: 1095
  helix: -0.26 (0.23), residues: 511
  sheet: -0.95 (0.43), residues: 121
  loop : -1.38 (0.27), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 916 
 HIS   0.010   0.002   HIS A 309 
 PHE   0.017   0.003   PHE A 652 
 TYR   0.036   0.003   TYR A 867 
 ARG   0.004   0.001   ARG A 392 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 140
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.8098 (mmm) cc_final: 0.7896 (mmt)
REVERT: A  334 PHE cc_start: 0.7970 (m-80) cc_final: 0.7442 (m-80)
REVERT: A  361 LEU cc_start: 0.7399 (mt) cc_final: 0.6802 (tt)
REVERT: A  426 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7440 (mptt)
REVERT: A  508 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8276 (mmtp)
REVERT: A  522 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7540 (pp20)
REVERT: A  553 ARG cc_start: 0.6697 (mmm-85) cc_final: 0.6475 (mmm-85)
REVERT: A  750 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7747 (mmm160)
REVERT: A  760 ASP cc_start: 0.7336 (p0) cc_final: 0.6996 (OUTLIER)
REVERT: A  826 TYR cc_start: 0.7550 (m-80) cc_final: 0.7297 (m-10)
REVERT: B   90 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.6919 (ttt)
REVERT: B  137 THR cc_start: 0.8491 (m) cc_final: 0.8212 (m)
REVERT: B  145 THR cc_start: 0.8241 (m) cc_final: 0.7827 (p)
REVERT: B  155 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7643 (pm20)
REVERT: B  176 ASN cc_start: 0.8522 (t0) cc_final: 0.8042 (t0)
REVERT: C   35 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7448 (mp)
  outliers start: 47
  outliers final: 22
  residues processed: 172
  average time/residue: 1.1429
  time to fit residues: 211.6722
Evaluate side-chains
  164 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 136
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  208 ASP
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  426 LYS
Chi-restraints excluded: chain A residue  451 SER
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  482 CYS
Chi-restraints excluded: chain A residue  508 LYS
Chi-restraints excluded: chain A residue  522 GLU
Chi-restraints excluded: chain A residue  635 SER
Chi-restraints excluded: chain A residue  643 THR
Chi-restraints excluded: chain A residue  667 VAL
Chi-restraints excluded: chain A residue  680 THR
Chi-restraints excluded: chain A residue  750 ARG
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  790 ASN
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain A residue  876 GLU
Chi-restraints excluded: chain B residue   90 MET
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain C residue    8 CYS
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain C residue   35 LEU
Chi-restraints excluded: chain D residue  124 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 100 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 105 optimal weight:    7.9990
   chunk 38 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0040
   chunk 98 optimal weight:    6.9990
   chunk 56 optimal weight:   10.0000
   chunk 43 optimal weight:    5.9990
   chunk 102 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   overall best weight:    1.7398

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

Flipped N/Q/H residues before XYZ refinement:
A 224 GLN
A 408 GLN
A 543 ASN
A 613 HIS
A 752 HIS
A 872 HIS
B 100 ASN
B 118 ASN
B 158 GLN
D 140 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.183153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.149641 restraints weight = 10299.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3737 rms_B_bonded: 1.94
r_work: 0.3556 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3438 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.4819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8992  Z= 0.199
  Angle     :  0.531   9.743  12222  Z= 0.283
  Chirality :  0.043   0.133   1393
  Planarity :  0.004   0.035   1555
  Dihedral  :  4.343  20.737   1204
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 20.85 %
    Favored  : 74.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -0.96 (0.25), residues: 1095
  helix:  0.05 (0.23), residues: 514
  sheet: -0.76 (0.43), residues: 121
  loop : -1.31 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 916 
 HIS   0.007   0.001   HIS A 309 
 PHE   0.013   0.002   PHE A 753 
 TYR   0.019   0.001   TYR A 867 
 ARG   0.003   0.000   ARG A 726 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 142
  time to evaluate  : 1.174 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 ILE cc_start: 0.8147 (mm) cc_final: 0.7656 (tt)
REVERT: A  217 TYR cc_start: 0.6914 (p90) cc_final: 0.6673 (p90)
REVERT: A  334 PHE cc_start: 0.7849 (m-80) cc_final: 0.7263 (m-80)
REVERT: A  361 LEU cc_start: 0.7434 (mt) cc_final: 0.6797 (tt)
REVERT: A  411 LYS cc_start: 0.8212 (ptmt) cc_final: 0.7831 (ptmm)
REVERT: A  508 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8284 (mmtp)
REVERT: A  522 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7420 (pp20)
REVERT: A  750 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7771 (mmm160)
REVERT: A  760 ASP cc_start: 0.7155 (p0) cc_final: 0.6834 (OUTLIER)
REVERT: A  811 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7226 (mm-30)
REVERT: B   90 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.7080 (tmm)
REVERT: B  118 ASN cc_start: 0.8680 (m-40) cc_final: 0.8448 (m-40)
REVERT: B  137 THR cc_start: 0.8539 (m) cc_final: 0.8271 (m)
REVERT: B  145 THR cc_start: 0.8114 (m) cc_final: 0.7754 (p)
REVERT: B  176 ASN cc_start: 0.8498 (t0) cc_final: 0.8171 (t0)
REVERT: B  179 ASN cc_start: 0.7635 (t0) cc_final: 0.7185 (t0)
REVERT: C    3 MET cc_start: 0.7294 (ttp) cc_final: 0.6528 (tpt)
  outliers start: 44
  outliers final: 18
  residues processed: 168
  average time/residue: 1.0354
  time to fit residues: 187.9309
Evaluate side-chains
  155 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 133
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  451 SER
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  482 CYS
Chi-restraints excluded: chain A residue  508 LYS
Chi-restraints excluded: chain A residue  522 GLU
Chi-restraints excluded: chain A residue  635 SER
Chi-restraints excluded: chain A residue  643 THR
Chi-restraints excluded: chain A residue  680 THR
Chi-restraints excluded: chain A residue  750 ARG
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain A residue  876 GLU
Chi-restraints excluded: chain A residue  924 MET
Chi-restraints excluded: chain A residue  929 THR
Chi-restraints excluded: chain B residue   90 MET
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain D residue  124 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0470
   chunk 57 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 46 optimal weight:    8.9990
   chunk 49 optimal weight:    2.9990
   chunk 3 optimal weight:    0.1980
   chunk 40 optimal weight:    0.9980
   chunk 107 optimal weight:   20.0000
   chunk 94 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   overall best weight:    1.4482

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

Flipped N/Q/H residues before XYZ refinement:
A 224 GLN
A 543 ASN
A 790 ASN
A 872 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.185538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.152192 restraints weight = 10144.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 1.92
r_work: 0.3551 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3432 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.4940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8992  Z= 0.185
  Angle     :  0.525  10.079  12222  Z= 0.279
  Chirality :  0.042   0.124   1393
  Planarity :  0.004   0.032   1555
  Dihedral  :  4.260  20.066   1204
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 20.64 %
    Favored  : 75.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -0.82 (0.25), residues: 1095
  helix:  0.18 (0.23), residues: 515
  sheet: -0.66 (0.44), residues: 121
  loop : -1.26 (0.27), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 916 
 HIS   0.007   0.001   HIS A 309 
 PHE   0.015   0.002   PHE A 415 
 TYR   0.031   0.001   TYR A 867 
 ARG   0.002   0.000   ARG A 726 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 134
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 ILE cc_start: 0.8141 (mm) cc_final: 0.7781 (tt)
REVERT: A  198 ASN cc_start: 0.8181 (m-40) cc_final: 0.7968 (m110)
REVERT: A  334 PHE cc_start: 0.7802 (m-80) cc_final: 0.7237 (m-80)
REVERT: A  361 LEU cc_start: 0.7305 (mt) cc_final: 0.6664 (tt)
REVERT: A  411 LYS cc_start: 0.8195 (ptmt) cc_final: 0.7826 (ptmm)
REVERT: A  508 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8268 (mmtp)
REVERT: A  624 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7981 (mpt-90)
REVERT: A  750 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7761 (mmm160)
REVERT: A  760 ASP cc_start: 0.7136 (p0) cc_final: 0.6847 (OUTLIER)
REVERT: A  811 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7272 (mm-30)
REVERT: B  137 THR cc_start: 0.8528 (m) cc_final: 0.8277 (m)
REVERT: B  145 THR cc_start: 0.8096 (m) cc_final: 0.7762 (p)
REVERT: B  164 SER cc_start: 0.7143 (m) cc_final: 0.6843 (t)
REVERT: B  179 ASN cc_start: 0.7672 (t0) cc_final: 0.7308 (t0)
REVERT: B  180 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6711 (mm)
REVERT: C    3 MET cc_start: 0.7317 (ttp) cc_final: 0.6544 (tpt)
REVERT: C   31 GLN cc_start: 0.7022 (tt0) cc_final: 0.6725 (tp-100)
  outliers start: 40
  outliers final: 24
  residues processed: 158
  average time/residue: 1.0575
  time to fit residues: 180.5008
Evaluate side-chains
  156 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 128
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  208 ASP
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  451 SER
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  482 CYS
Chi-restraints excluded: chain A residue  508 LYS
Chi-restraints excluded: chain A residue  549 SER
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  624 ARG
Chi-restraints excluded: chain A residue  635 SER
Chi-restraints excluded: chain A residue  643 THR
Chi-restraints excluded: chain A residue  667 VAL
Chi-restraints excluded: chain A residue  680 THR
Chi-restraints excluded: chain A residue  750 ARG
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain A residue  876 GLU
Chi-restraints excluded: chain A residue  929 THR
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain C residue    8 CYS
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   52 MET
Chi-restraints excluded: chain D residue  124 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 94 optimal weight:   10.0000
   chunk 41 optimal weight:   10.0000
   chunk 7 optimal weight:    0.8980
   chunk 90 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   chunk 72 optimal weight:    9.9990
   chunk 99 optimal weight:    4.9990
   chunk 14 optimal weight:   20.0000
   chunk 101 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 224 GLN
A 543 ASN
A 600 ASN
A 872 HIS
C  19 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.183096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.149266 restraints weight = 10181.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3716 rms_B_bonded: 1.97
r_work: 0.3536 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3418 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.5142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8992  Z= 0.286
  Angle     :  0.577  10.662  12222  Z= 0.306
  Chirality :  0.045   0.129   1393
  Planarity :  0.004   0.032   1555
  Dihedral  :  4.500  22.563   1204
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 19.71 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -1.02 (0.24), residues: 1095
  helix:  0.02 (0.23), residues: 515
  sheet: -0.70 (0.44), residues: 121
  loop : -1.39 (0.27), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 916 
 HIS   0.008   0.001   HIS A 309 
 PHE   0.014   0.002   PHE A 652 
 TYR   0.032   0.002   TYR A 867 
 ARG   0.003   0.001   ARG A 651 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 128
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 ILE cc_start: 0.8162 (mm) cc_final: 0.7715 (tt)
REVERT: A  196 MET cc_start: 0.7790 (mtp) cc_final: 0.7492 (mtm)
REVERT: A  198 ASN cc_start: 0.8205 (m-40) cc_final: 0.7964 (m110)
REVERT: A  260 ASP cc_start: 0.7266 (t0) cc_final: 0.6822 (m-30)
REVERT: A  334 PHE cc_start: 0.7871 (m-80) cc_final: 0.7381 (m-80)
REVERT: A  508 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8323 (mmtp)
REVERT: A  522 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7466 (pm20)
REVERT: A  624 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8044 (mpt-90)
REVERT: A  718 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8540 (ttpt)
REVERT: A  750 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7763 (mmm160)
REVERT: A  760 ASP cc_start: 0.7331 (p0) cc_final: 0.6998 (OUTLIER)
REVERT: A  811 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7383 (mm-30)
REVERT: A  887 TYR cc_start: 0.7985 (t80) cc_final: 0.7708 (t80)
REVERT: B   90 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.6900 (tmt)
REVERT: B  137 THR cc_start: 0.8515 (m) cc_final: 0.8271 (m)
REVERT: B  145 THR cc_start: 0.8162 (m) cc_final: 0.7811 (p)
REVERT: B  179 ASN cc_start: 0.7756 (t0) cc_final: 0.7439 (t0)
REVERT: B  180 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6595 (mm)
REVERT: C    3 MET cc_start: 0.7366 (ttp) cc_final: 0.6669 (tpt)
REVERT: C   31 GLN cc_start: 0.7153 (tt0) cc_final: 0.6832 (tp40)
REVERT: C   43 LYS cc_start: 0.6840 (OUTLIER) cc_final: 0.6386 (mtmp)
  outliers start: 48
  outliers final: 29
  residues processed: 161
  average time/residue: 1.0972
  time to fit residues: 190.6401
Evaluate side-chains
  162 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 125
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  332 LYS
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  415 PHE
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  451 SER
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  482 CYS
Chi-restraints excluded: chain A residue  508 LYS
Chi-restraints excluded: chain A residue  522 GLU
Chi-restraints excluded: chain A residue  549 SER
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  624 ARG
Chi-restraints excluded: chain A residue  635 SER
Chi-restraints excluded: chain A residue  643 THR
Chi-restraints excluded: chain A residue  667 VAL
Chi-restraints excluded: chain A residue  680 THR
Chi-restraints excluded: chain A residue  718 LYS
Chi-restraints excluded: chain A residue  750 ARG
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain A residue  818 MET
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain A residue  876 GLU
Chi-restraints excluded: chain A residue  924 MET
Chi-restraints excluded: chain A residue  929 THR
Chi-restraints excluded: chain B residue   90 MET
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain C residue    8 CYS
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   52 MET
Chi-restraints excluded: chain D residue  124 THR
Chi-restraints excluded: chain D residue  186 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0670
   chunk 89 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9990
   chunk 87 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 46 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 108 optimal weight:    7.9990
   overall best weight:    1.8126

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

Flipped N/Q/H residues before XYZ refinement:
A 191 GLN
A 543 ASN
A 872 HIS
B 158 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.182624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.148775 restraints weight = 10384.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3731 rms_B_bonded: 1.81
r_work: 0.3567 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3450 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.5239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8992  Z= 0.203
  Angle     :  0.530  10.343  12222  Z= 0.281
  Chirality :  0.043   0.126   1393
  Planarity :  0.004   0.033   1555
  Dihedral  :  4.353  20.267   1204
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 20.54 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -0.89 (0.25), residues: 1095
  helix:  0.17 (0.23), residues: 514
  sheet: -0.69 (0.44), residues: 121
  loop : -1.37 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 916 
 HIS   0.007   0.001   HIS A 309 
 PHE   0.012   0.002   PHE A 920 
 TYR   0.026   0.002   TYR A 867 
 ARG   0.002   0.000   ARG A 726 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 135
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 ILE cc_start: 0.8193 (mm) cc_final: 0.7789 (tt)
REVERT: A  196 MET cc_start: 0.7816 (mtp) cc_final: 0.7509 (mtm)
REVERT: A  198 ASN cc_start: 0.8172 (m-40) cc_final: 0.7918 (m110)
REVERT: A  260 ASP cc_start: 0.7078 (t0) cc_final: 0.6744 (m-30)
REVERT: A  334 PHE cc_start: 0.7815 (m-80) cc_final: 0.7340 (m-80)
REVERT: A  508 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8283 (mmtp)
REVERT: A  718 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8495 (ttpt)
REVERT: A  750 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7748 (mmm160)
REVERT: A  760 ASP cc_start: 0.7209 (p0) cc_final: 0.6887 (OUTLIER)
REVERT: A  811 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7328 (mm-30)
REVERT: B  137 THR cc_start: 0.8512 (m) cc_final: 0.8277 (m)
REVERT: B  145 THR cc_start: 0.8021 (m) cc_final: 0.7691 (p)
REVERT: B  179 ASN cc_start: 0.7713 (t0) cc_final: 0.7428 (t0)
REVERT: B  180 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6925 (mt)
REVERT: C    3 MET cc_start: 0.7388 (ttp) cc_final: 0.6612 (tpt)
REVERT: C   31 GLN cc_start: 0.7075 (tt0) cc_final: 0.6740 (tp-100)
  outliers start: 43
  outliers final: 28
  residues processed: 161
  average time/residue: 1.0744
  time to fit residues: 186.2721
Evaluate side-chains
  163 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 131
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  332 LYS
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  415 PHE
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  451 SER
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  482 CYS
Chi-restraints excluded: chain A residue  508 LYS
Chi-restraints excluded: chain A residue  549 SER
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  635 SER
Chi-restraints excluded: chain A residue  643 THR
Chi-restraints excluded: chain A residue  667 VAL
Chi-restraints excluded: chain A residue  680 THR
Chi-restraints excluded: chain A residue  718 LYS
Chi-restraints excluded: chain A residue  750 ARG
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain A residue  876 GLU
Chi-restraints excluded: chain A residue  924 MET
Chi-restraints excluded: chain A residue  929 THR
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain C residue    8 CYS
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain D residue  124 THR
Chi-restraints excluded: chain D residue  186 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0970
   chunk 105 optimal weight:    0.1980
   chunk 8 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 69 optimal weight:    6.9990
   chunk 107 optimal weight:    8.9990
   chunk 26 optimal weight:    0.5980
   chunk 106 optimal weight:    8.9990
   chunk 42 optimal weight:    5.9990
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
A 191 GLN
A 543 ASN
A 872 HIS
B 158 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.185343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.152532 restraints weight = 10259.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3756 rms_B_bonded: 1.83
r_work: 0.3579 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3461 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.5344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8992  Z= 0.175
  Angle     :  0.520  10.397  12222  Z= 0.276
  Chirality :  0.042   0.126   1393
  Planarity :  0.003   0.034   1555
  Dihedral  :  4.221  20.982   1204
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 20.75 %
    Favored  : 75.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -0.79 (0.25), residues: 1095
  helix:  0.27 (0.24), residues: 514
  sheet: -0.66 (0.44), residues: 121
  loop : -1.33 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 916 
 HIS   0.007   0.001   HIS A 309 
 PHE   0.012   0.001   PHE A 920 
 TYR   0.023   0.001   TYR A 867 
 ARG   0.002   0.000   ARG A 726 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 136
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 ILE cc_start: 0.8243 (mm) cc_final: 0.7855 (tt)
REVERT: A  196 MET cc_start: 0.7825 (mtp) cc_final: 0.7526 (mtm)
REVERT: A  198 ASN cc_start: 0.8187 (m-40) cc_final: 0.7964 (m110)
REVERT: A  260 ASP cc_start: 0.7034 (t0) cc_final: 0.6647 (m-30)
REVERT: A  334 PHE cc_start: 0.7799 (m-80) cc_final: 0.7337 (m-80)
REVERT: A  494 ILE cc_start: 0.8543 (mm) cc_final: 0.8237 (mp)
REVERT: A  508 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8306 (mmtp)
REVERT: A  624 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7990 (mpt-90)
REVERT: A  718 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8454 (ttpt)
REVERT: A  750 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7793 (mmm160)
REVERT: A  760 ASP cc_start: 0.7161 (p0) cc_final: 0.6871 (OUTLIER)
REVERT: B  137 THR cc_start: 0.8442 (m) cc_final: 0.8207 (m)
REVERT: B  145 THR cc_start: 0.8098 (m) cc_final: 0.7772 (p)
REVERT: B  179 ASN cc_start: 0.7700 (t0) cc_final: 0.7423 (t0)
REVERT: C    3 MET cc_start: 0.7364 (ttp) cc_final: 0.6569 (tpt)
REVERT: C   31 GLN cc_start: 0.7134 (tt0) cc_final: 0.6751 (tp-100)
  outliers start: 37
  outliers final: 27
  residues processed: 157
  average time/residue: 1.0797
  time to fit residues: 182.7876
Evaluate side-chains
  163 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 133
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  332 LYS
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  415 PHE
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  451 SER
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  482 CYS
Chi-restraints excluded: chain A residue  508 LYS
Chi-restraints excluded: chain A residue  549 SER
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  624 ARG
Chi-restraints excluded: chain A residue  635 SER
Chi-restraints excluded: chain A residue  643 THR
Chi-restraints excluded: chain A residue  667 VAL
Chi-restraints excluded: chain A residue  680 THR
Chi-restraints excluded: chain A residue  718 LYS
Chi-restraints excluded: chain A residue  750 ARG
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  761 ASP
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain A residue  876 GLU
Chi-restraints excluded: chain A residue  929 THR
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain C residue    8 CYS
Chi-restraints excluded: chain D residue  124 THR
Chi-restraints excluded: chain D residue  186 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 1 optimal weight:    7.9990
   chunk 64 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   chunk 98 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 97 optimal weight:    5.9990
   chunk 86 optimal weight:    0.1980
   chunk 58 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
A 191 GLN
A 543 ASN
A 791 ASN
A 872 HIS
B 158 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.184861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.151833 restraints weight = 10234.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3743 rms_B_bonded: 1.88
r_work: 0.3566 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3448 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.5416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8992  Z= 0.189
  Angle     :  0.531  11.116  12222  Z= 0.281
  Chirality :  0.042   0.156   1393
  Planarity :  0.003   0.033   1555
  Dihedral  :  4.232  19.661   1204
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 21.06 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -0.86 (0.25), residues: 1095
  helix:  0.19 (0.23), residues: 520
  sheet: -0.63 (0.45), residues: 121
  loop : -1.36 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 916 
 HIS   0.007   0.001   HIS A 309 
 PHE   0.014   0.001   PHE A 753 
 TYR   0.024   0.001   TYR A 867 
 ARG   0.002   0.000   ARG A 726 

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 136
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 ILE cc_start: 0.8256 (mm) cc_final: 0.7934 (tt)
REVERT: A  196 MET cc_start: 0.7841 (mtp) cc_final: 0.7525 (mtm)
REVERT: A  198 ASN cc_start: 0.8227 (m-40) cc_final: 0.8012 (m110)
REVERT: A  260 ASP cc_start: 0.7061 (t0) cc_final: 0.6681 (m-30)
REVERT: A  334 PHE cc_start: 0.7828 (m-80) cc_final: 0.7377 (m-80)
REVERT: A  411 LYS cc_start: 0.8163 (ptmm) cc_final: 0.7739 (ptmm)
REVERT: A  508 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8298 (mmtp)
REVERT: A  624 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8014 (mpt-90)
REVERT: A  718 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8457 (ttpt)
REVERT: A  750 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7796 (mmm160)
REVERT: A  760 ASP cc_start: 0.7001 (p0) cc_final: 0.6711 (OUTLIER)
REVERT: B  145 THR cc_start: 0.8213 (m) cc_final: 0.7885 (p)
REVERT: B  164 SER cc_start: 0.7192 (m) cc_final: 0.6940 (t)
REVERT: B  179 ASN cc_start: 0.7733 (t0) cc_final: 0.7466 (t0)
REVERT: C    3 MET cc_start: 0.7352 (ttp) cc_final: 0.6601 (tpt)
REVERT: C   31 GLN cc_start: 0.7238 (tt0) cc_final: 0.6825 (tp-100)
  outliers start: 35
  outliers final: 26
  residues processed: 159
  average time/residue: 1.0852
  time to fit residues: 186.5530
Evaluate side-chains
  161 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 132
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  332 LYS
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  415 PHE
Chi-restraints excluded: chain A residue  424 VAL
Chi-restraints excluded: chain A residue  451 SER
Chi-restraints excluded: chain A residue  477 ASP
Chi-restraints excluded: chain A residue  482 CYS
Chi-restraints excluded: chain A residue  508 LYS
Chi-restraints excluded: chain A residue  549 SER
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  624 ARG
Chi-restraints excluded: chain A residue  635 SER
Chi-restraints excluded: chain A residue  643 THR
Chi-restraints excluded: chain A residue  667 VAL
Chi-restraints excluded: chain A residue  680 THR
Chi-restraints excluded: chain A residue  718 LYS
Chi-restraints excluded: chain A residue  750 ARG
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain A residue  876 GLU
Chi-restraints excluded: chain A residue  929 THR
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain C residue    8 CYS
Chi-restraints excluded: chain D residue  124 THR
Chi-restraints excluded: chain D residue  186 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 103 optimal weight:   10.0000
   chunk 62 optimal weight:    7.9990
   chunk 100 optimal weight:    8.9990
   chunk 66 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 95 optimal weight:    2.9990
   chunk 73 optimal weight:    7.9990
   chunk 50 optimal weight:    6.9990
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 191 GLN
A 543 ASN
A 752 HIS
A 872 HIS
A 874 ASN
B 158 GLN
C  63 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.178271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.143687 restraints weight = 10209.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3667 rms_B_bonded: 1.91
r_work: 0.3521 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3407 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.5585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   8992  Z= 0.401
  Angle     :  0.650  10.911  12222  Z= 0.345
  Chirality :  0.048   0.155   1393
  Planarity :  0.004   0.035   1555
  Dihedral  :  4.818  23.623   1204
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 20.54 %
    Favored  : 75.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.24), residues: 1095
  helix: -0.21 (0.23), residues: 521
  sheet: -0.85 (0.43), residues: 134
  loop : -1.57 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 162 
 HIS   0.009   0.002   HIS A 309 
 PHE   0.016   0.003   PHE A 652 
 TYR   0.032   0.003   TYR A 867 
 ARG   0.005   0.001   ARG B 190 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6909.47 seconds
wall clock time: 122 minutes 19.62 seconds (7339.62 seconds total)