Starting phenix.real_space_refine
on Wed Mar  4 07:04:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vgj_31971/03_2026/7vgj_31971.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vgj_31971/03_2026/7vgj_31971.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vgj_31971/03_2026/7vgj_31971.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vgj_31971/03_2026/7vgj_31971.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vgj_31971/03_2026/7vgj_31971.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vgj_31971/03_2026/7vgj_31971.cif"
  }
  resolution = 3.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.002
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
     P       1      5.49       5
     S      57      5.16       5
     C    7413      2.51       5
     N    1904      2.21       5
     O    2085      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11460
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 8753
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1084, 8753
          Classifications: {'peptide': 1084}
          Link IDs: {'PTRANS': 27, 'TRANS': 1056}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "B"
      Number of atoms: 2653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2653
          Classifications: {'peptide': 330}
          Link IDs: {'PTRANS': 25, 'TRANS': 304}
    Chain: "A"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 54
          Classifications: {'peptide': 1}
  Time building chain proxies: 2.33, per 1000 atoms: 0.20
  Number of scatterers: 11460
  At special positions: 0
  Unit cell: (100.287, 107.378, 172.21, 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)
     S      57     16.00
     P       1     15.00
     O    2085      8.00
     N    1904      7.00
     C    7413      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  97 " - pdb=" SG  CYS B 105 " distance=2.03

  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: 0.97
  Conformation dependent library (CDL) restraints added in 537.6 milliseconds
  

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2672

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 10 sheets defined
      44.8% alpha, 10.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 106 through 116
      removed outlier: 4.319A  pdb=" N   MET A 110 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 132
    Processing helix  chain 'A' and resid 144 through 164
      removed outlier: 3.732A  pdb=" N   VAL A 150 " --> pdb=" O   VAL A 146 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL A 151 " --> pdb=" O   PRO A 147 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU A 152 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   THR A 155 " --> pdb=" O   VAL A 151 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   ALA A 156 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 174
      removed outlier: 4.194A  pdb=" N   LYS A 168 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 223
    Processing helix  chain 'A' and resid 244 through 248
      removed outlier: 3.768A  pdb=" N   GLN A 248 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 258
    Processing helix  chain 'A' and resid 318 through 322
    Processing helix  chain 'A' and resid 331 through 367
      removed outlier: 3.777A  pdb=" N   TYR A 335 " --> pdb=" O   THR A 331 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 390
      removed outlier: 3.821A  pdb=" N   TRP A 390 " --> pdb=" O   PHE A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 421
      removed outlier: 4.404A  pdb=" N   GLU A 409 " --> pdb=" O   TYR A 405 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   HIS A 417 " --> pdb=" O   LEU A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 426
    Processing helix  chain 'A' and resid 443 through 447
    Processing helix  chain 'A' and resid 454 through 459
      removed outlier: 3.925A  pdb=" N   THR A 458 " --> pdb=" O   ASP A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 519
      removed outlier: 4.889A  pdb=" N   ILE A 516 " --> pdb=" O   LEU A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 534
    Processing helix  chain 'A' and resid 555 through 565
    Processing helix  chain 'A' and resid 621 through 626
    Processing helix  chain 'A' and resid 634 through 647
      removed outlier: 4.114A  pdb=" N   GLU A 638 " --> pdb=" O   PRO A 634 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ILE A 645 " --> pdb=" O   ASP A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 678
      removed outlier: 4.089A  pdb=" N   LYS A 672 " --> pdb=" O   GLU A 668 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   VAL A 678 " --> pdb=" O   MET A 674 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 692
      removed outlier: 3.556A  pdb=" N   VAL A 690 " --> pdb=" O   ALA A 686 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 724
    Processing helix  chain 'A' and resid 735 through 746
      removed outlier: 3.614A  pdb=" N   ALA A 739 " --> pdb=" O   LYS A 735 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   PHE A 744 " --> pdb=" O   GLU A 740 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 757 through 769
    Processing helix  chain 'A' and resid 803 through 811
    Processing helix  chain 'A' and resid 841 through 846
    Processing helix  chain 'A' and resid 848 through 859
    Processing helix  chain 'A' and resid 869 through 883
      removed outlier: 3.682A  pdb=" N   ALA A 874 " --> pdb=" O   PRO A 870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 895 through 900
      removed outlier: 4.030A  pdb=" N   ASN A 899 " --> pdb=" O   ASN A 896 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 917 through 922
    Processing helix  chain 'A' and resid 931 through 936
    Processing helix  chain 'A' and resid 939 through 969
      removed outlier: 4.082A  pdb=" N   PHE A 955 " --> pdb=" O   LEU A 951 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   TYR A 956 " --> pdb=" O   ARG A 952 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   ASN A 958 " --> pdb=" O   PHE A 954 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   PHE A 961 " --> pdb=" O   LYS A 957 " (cutoff:3.500A)
      removed outlier: 5.673A  pdb=" N   VAL A 964 " --> pdb=" O   ALA A 960 " (cutoff:3.500A)
      removed outlier: 5.328A  pdb=" N   HIS A 965 " --> pdb=" O   PHE A 961 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   PHE A 966 " --> pdb=" O   THR A 962 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 973
      removed outlier: 3.878A  pdb=" N   GLY A 973 " --> pdb=" O   PHE A 970 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 970 through 973'
    Processing helix  chain 'A' and resid 981 through 986
      removed outlier: 4.096A  pdb=" N   THR A 986 " --> pdb=" O   ASP A 982 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 987 through 992
    Processing helix  chain 'A' and resid 994 through 1004
    Processing helix  chain 'A' and resid 1008 through 1015
    Processing helix  chain 'A' and resid 1019 through 1025
      removed outlier: 3.982A  pdb=" N   GLN A1023 " --> pdb=" O   TYR A1019 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1031 through 1056
      removed outlier: 3.768A  pdb=" N   LEU A1042 " --> pdb=" O   LEU A1038 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   THR A1043 " --> pdb=" O   HIS A1039 " (cutoff:3.500A)
      Proline residue:  A1051  - end of helix
    Processing helix  chain 'A' and resid 1068 through 1073
    Processing helix  chain 'A' and resid 1073 through 1092
      removed outlier: 4.244A  pdb=" N   ALA A1079 " --> pdb=" O   THR A1075 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ASN A1085 " --> pdb=" O   VAL A1081 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1096 through 1117
    Processing helix  chain 'A' and resid 1119 through 1124
      removed outlier: 3.895A  pdb=" N   HIS A1123 " --> pdb=" O   SER A1119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1135 through 1140
    Processing helix  chain 'A' and resid 1148 through 1171
      Proline residue:  A1159  - end of helix
    Processing helix  chain 'A' and resid 1173 through 1181
      removed outlier: 4.075A  pdb=" N   HIS A1181 " --> pdb=" O   LYS A1177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 62
      removed outlier: 4.013A  pdb=" N   LEU B  54 " --> pdb=" O   ALA B  50 " (cutoff:3.500A)
      Proline residue:  B  55  - end of helix
    Processing helix  chain 'B' and resid 64 through 77
      removed outlier: 4.038A  pdb=" N   THR B  74 " --> pdb=" O   GLY B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 98
    Processing helix  chain 'B' and resid 134 through 139
      removed outlier: 3.575A  pdb=" N   LYS B 139 " --> pdb=" O   ARG B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 148
      removed outlier: 3.715A  pdb=" N   GLY B 148 " --> pdb=" O   SER B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 155
      removed outlier: 3.693A  pdb=" N   LEU B 154 " --> pdb=" O   SER B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 180
    Processing helix  chain 'B' and resid 227 through 231
      removed outlier: 3.978A  pdb=" N   LYS B 231 " --> pdb=" O   GLU B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 246
      removed outlier: 3.570A  pdb=" N   MET B 245 " --> pdb=" O   PRO B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 265
    Processing helix  chain 'B' and resid 325 through 354
      removed outlier: 3.915A  pdb=" N   GLY B 329 " --> pdb=" O   ASN B 325 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL B 344 " --> pdb=" O   PHE B 340 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL B 345 " --> pdb=" O   LEU B 341 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 189
      removed outlier: 4.089A  pdb=" N   GLU A 179 " --> pdb=" O   ARG A 201 " (cutoff:3.500A)
      removed outlier: 5.229A  pdb=" N   VAL A 199 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLY A 308 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 189
      removed outlier: 4.089A  pdb=" N   GLU A 179 " --> pdb=" O   ARG A 201 " (cutoff:3.500A)
      removed outlier: 5.229A  pdb=" N   VAL A 199 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLY A 308 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 238 through 240
      removed outlier: 4.140A  pdb=" N   VAL A 299 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 799 through 802
      removed outlier: 5.690A  pdb=" N   LEU A 799 " --> pdb=" O   ILE A 864 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   CYS A 866 " --> pdb=" O   LEU A 799 " (cutoff:3.500A)
      removed outlier: 5.737A  pdb=" N   ILE A 801 " --> pdb=" O   CYS A 866 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   VAL A 863 " --> pdb=" O   ILE A 728 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   ILE A 451 " --> pdb=" O   TRP A 729 " (cutoff:3.500A)
      removed outlier: 7.254A  pdb=" N   LEU A 731 " --> pdb=" O   ILE A 451 " (cutoff:3.500A)
      removed outlier: 5.615A  pdb=" N   SER A 453 " --> pdb=" O   LEU A 731 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   TYR A 450 " --> pdb=" O   LEU A 889 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   ILE A 891 " --> pdb=" O   TYR A 450 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   PHE A 452 " --> pdb=" O   ILE A 891 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   THR A 888 " --> pdb=" O   ILE A 906 " (cutoff:3.500A)
      removed outlier: 7.956A  pdb=" N   VAL A 908 " --> pdb=" O   THR A 888 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   ALA A 890 " --> pdb=" O   VAL A 908 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   ILE A 910 " --> pdb=" O   ALA A 890 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   GLY A 892 " --> pdb=" O   ILE A 910 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 470 through 471
    Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 540
    Processing sheet with id=AA7, first strand: chain 'A' and resid 569 through 570
      removed outlier: 4.134A  pdb=" N   THR A 578 " --> pdb=" O   LEU A 570 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   ILE A 606 " --> pdb=" O   LEU A 591 " (cutoff:3.500A)
      removed outlier: 5.849A  pdb=" N   ILE A 593 " --> pdb=" O   SER A 604 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   SER A 604 " --> pdb=" O   ILE A 593 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 652 through 658
      removed outlier: 5.791A  pdb=" N   TYR A 658 " --> pdb=" O   LEU A 700 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   LEU A 700 " --> pdb=" O   TYR A 658 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 81 through 82
      removed outlier: 4.070A  pdb=" N   ILE B  81 " --> pdb=" O   LEU B 315 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU B 315 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   TYR B 125 " --> pdb=" O   LEU B 275 " (cutoff:3.500A)
      removed outlier: 5.418A  pdb=" N   LEU B 275 " --> pdb=" O   TYR B 125 " (cutoff:3.500A)
      removed outlier: 7.325A  pdb=" N   LEU B 127 " --> pdb=" O   ARG B 273 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   ARG B 273 " --> pdb=" O   LEU B 127 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 105 through 113
      removed outlier: 4.014A  pdb=" N   CYS B 105 " --> pdb=" O   TYR B 300 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   ARG B 293 " --> pdb=" O   ILE B 191 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE B 191 " --> pdb=" O   ARG B 293 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   THR B 185 " --> pdb=" O   THR B 299 " (cutoff:3.500A)

    431 hydrogen bonds defined for protein.
    1200 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: 1.98

  Time building geometry restraints manager: 1.31 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1845
        1.30 -     1.43: 3230
        1.43 -     1.56: 6569
        1.56 -     1.69: 2
        1.69 -     1.81: 87
  Bond restraints: 11733
  Sorted by residual:
  bond pdb=" N   LEU A 294 "
       pdb=" CA  LEU A 294 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.036 1.23e-02 6.61e+03 8.38e+00
  bond pdb=" C38 P5S A1301 "
       pdb=" O37 P5S A1301 "
    ideal  model  delta    sigma   weight residual
    1.345  1.396 -0.051 2.00e-02 2.50e+03 6.60e+00
  bond pdb=" N   HIS A 510 "
       pdb=" CA  HIS A 510 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.28e-02 6.10e+03 6.53e+00
  bond pdb=" C17 P5S A1301 "
       pdb=" O19 P5S A1301 "
    ideal  model  delta    sigma   weight residual
    1.351  1.401 -0.050 2.00e-02 2.50e+03 6.30e+00
  bond pdb=" N   ASP A 454 "
       pdb=" CA  ASP A 454 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.22e-02 6.72e+03 6.11e+00
  ... (remaining 11728 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.70: 15572
        2.70 -     5.39: 271
        5.39 -     8.09: 36
        8.09 -    10.79: 9
       10.79 -    13.49: 2
  Bond angle restraints: 15890
  Sorted by residual:
  angle pdb=" CA  PRO B  90 "
        pdb=" N   PRO B  90 "
        pdb=" CD  PRO B  90 "
      ideal   model   delta    sigma   weight residual
     112.00  105.18    6.82 1.40e+00 5.10e-01 2.37e+01
  angle pdb=" O13 P5S A1301 "
        pdb=" P12 P5S A1301 "
        pdb=" O15 P5S A1301 "
      ideal   model   delta    sigma   weight residual
     121.25  107.76   13.49 3.00e+00 1.11e-01 2.02e+01
  angle pdb=" N   PRO B  90 "
        pdb=" CD  PRO B  90 "
        pdb=" CG  PRO B  90 "
      ideal   model   delta    sigma   weight residual
     103.20   96.59    6.61 1.50e+00 4.44e-01 1.94e+01
  angle pdb=" N   ASP A 289 "
        pdb=" CA  ASP A 289 "
        pdb=" C   ASP A 289 "
      ideal   model   delta    sigma   weight residual
     108.19  113.31   -5.12 1.29e+00 6.01e-01 1.58e+01
  angle pdb=" CA  LEU A1125 "
        pdb=" CB  LEU A1125 "
        pdb=" CG  LEU A1125 "
      ideal   model   delta    sigma   weight residual
     116.30  129.06  -12.76 3.50e+00 8.16e-02 1.33e+01
  ... (remaining 15885 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.81: 6817
       33.81 -    67.61: 146
       67.61 -   101.42: 22
      101.42 -   135.22: 3
      135.22 -   169.03: 3
  Dihedral angle restraints: 6991
    sinusoidal: 2845
      harmonic: 4146
  Sorted by residual:
  dihedral pdb=" CA  ILE B 171 "
           pdb=" C   ILE B 171 "
           pdb=" N   ALA B 172 "
           pdb=" CA  ALA B 172 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.28  -27.72     0      5.00e+00 4.00e-02 3.07e+01
  dihedral pdb=" CA  THR A 398 "
           pdb=" C   THR A 398 "
           pdb=" N   MET A 399 "
           pdb=" CA  MET A 399 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.47   25.53     0      5.00e+00 4.00e-02 2.61e+01
  dihedral pdb=" CA  GLU A 649 "
           pdb=" C   GLU A 649 "
           pdb=" N   THR A 650 "
           pdb=" CA  THR A 650 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.15  -23.85     0      5.00e+00 4.00e-02 2.28e+01
  ... (remaining 6988 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1215
       0.048 -    0.097: 438
       0.097 -    0.145: 90
       0.145 -    0.194: 11
       0.194 -    0.242: 5
  Chirality restraints: 1759
  Sorted by residual:
  chirality pdb=" CB  ILE A 181 "
            pdb=" CA  ILE A 181 "
            pdb=" CG1 ILE A 181 "
            pdb=" CG2 ILE A 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CB  ILE A 394 "
            pdb=" CA  ILE A 394 "
            pdb=" CG1 ILE A 394 "
            pdb=" CG2 ILE A 394 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  GLU B 161 "
            pdb=" N   GLU B 161 "
            pdb=" C   GLU B 161 "
            pdb=" CB  GLU B 161 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.12e+00
  ... (remaining 1756 not shown)

  Planarity restraints: 2010
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 133 "    0.047 5.00e-02 4.00e+02   7.01e-02 7.87e+00
        pdb=" N   PRO A 134 "   -0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO A 134 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 134 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B  89 "    0.045 5.00e-02 4.00e+02   6.57e-02 6.91e+00
        pdb=" N   PRO B  90 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO B  90 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B  90 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 302 "   -0.012 2.00e-02 2.50e+03   1.63e-02 5.31e+00
        pdb=" CG  TYR B 302 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 302 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 302 "   -0.020 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 302 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 302 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 302 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR B 302 "    0.001 2.00e-02 2.50e+03
  ... (remaining 2007 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 719
        2.71 -     3.26: 13045
        3.26 -     3.80: 18684
        3.80 -     4.35: 23232
        4.35 -     4.90: 36967
  Nonbonded interactions: 92647
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 238 "
            pdb=" O   PHE A 239 "
     model   vdw
     2.160 3.120
  nonbonded pdb=" O   PRO B 290 "
            pdb=" OH  TYR B 294 "
     model   vdw
     2.168 3.040
  nonbonded pdb=" NZ  LYS A 240 "
            pdb=" O   ILE A 293 "
     model   vdw
     2.197 3.120
  nonbonded pdb=" NZ  LYS B 235 "
            pdb=" O   PRO B 236 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" O   TYR A 992 "
            pdb=" OG  SER A1106 "
     model   vdw
     2.205 3.040
  ... (remaining 92642 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.390
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
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      :  0.007   0.079  11734  Z= 0.317
  Angle     :  0.917  13.487  15892  Z= 0.481
  Chirality :  0.051   0.242   1759
  Planarity :  0.005   0.070   2010
  Dihedral  : 16.170 169.027   4316
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 25.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.43 %
    Favored  : 83.57 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  0.32 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.55 (0.21), residues: 1406
  helix: -1.32 (0.21), residues: 531
  sheet: -2.05 (0.44), residues: 142
  loop : -3.34 (0.21), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 218 
 TYR   0.037   0.003   TYR B 302 
 PHE   0.019   0.002   PHE A 207 
 TRP   0.025   0.002   TRP A 191 
 HIS   0.007   0.002   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00704 (11733)
  covalent geometry    : angle       0.91747 (15890)
  SS BOND              : bond        0.00377 (    1)
  SS BOND              : angle       0.32632 (    2)
  hydrogen bonds       : bond        0.16119 (  424)
  hydrogen bonds       : angle       7.88324 ( 1200)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 120
  time to evaluate  : 0.467 
Fit side-chains
TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it.
REVERT: A  237 LEU cc_start: 0.8410 (tp) cc_final: 0.7599 (tp)
REVERT: A  467 LYS cc_start: 0.8593 (tppt) cc_final: 0.8159 (tppp)
REVERT: A  538 MET cc_start: 0.8515 (mpp) cc_final: 0.8052 (mpp)
REVERT: A  875 MET cc_start: 0.8649 (tmm) cc_final: 0.8390 (tmm)
REVERT: A 1113 ILE cc_start: 0.6186 (tp) cc_final: 0.5959 (tp)
REVERT: B  163 TYR cc_start: 0.7419 (p90) cc_final: 0.6791 (p90)
REVERT: B  314 ILE cc_start: 0.9068 (pt) cc_final: 0.8411 (pt)
  outliers start: 6
  outliers final: 2
  residues processed: 126
  average time/residue: 0.0818
  time to fit residues: 16.4021
Evaluate side-chains
  104 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 102
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  510 HIS
Chi-restraints excluded: chain A residue  692 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    0.0170
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    9.9990
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.1824

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
** A 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 741 ASN
** A 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1061 GLN
** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 147 ASN
B 183 ASN
** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.096867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.069143 restraints weight = 40342.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.071270 restraints weight = 21251.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.072600 restraints weight = 14240.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.073366 restraints weight = 11344.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.073851 restraints weight = 10001.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.1411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11734  Z= 0.137
  Angle     :  0.715  10.650  15892  Z= 0.362
  Chirality :  0.045   0.179   1759
  Planarity :  0.004   0.044   2010
  Dihedral  : 11.753 169.061   1605
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 15.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.17 %
    Favored  : 88.83 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  9.10 %
    Favored  : 89.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.92 (0.22), residues: 1406
  helix: -0.73 (0.22), residues: 562
  sheet: -1.48 (0.46), residues: 135
  loop : -3.16 (0.22), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 218 
 TYR   0.021   0.002   TYR A 476 
 PHE   0.019   0.002   PHE B 217 
 TRP   0.016   0.001   TRP A 191 
 HIS   0.006   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (11733)
  covalent geometry    : angle       0.71553 (15890)
  SS BOND              : bond        0.00301 (    1)
  SS BOND              : angle       0.33244 (    2)
  hydrogen bonds       : bond        0.04899 (  424)
  hydrogen bonds       : angle       5.98284 ( 1200)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 139
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLU A 692 " (corrupted residue). Skipping it.
REVERT: A  130 LEU cc_start: 0.8894 (tt) cc_final: 0.8634 (tt)
REVERT: A  211 ASP cc_start: 0.7599 (m-30) cc_final: 0.7390 (m-30)
REVERT: A  467 LYS cc_start: 0.9130 (tppt) cc_final: 0.8722 (tptp)
REVERT: A  538 MET cc_start: 0.8166 (mpp) cc_final: 0.7586 (mpp)
REVERT: A  720 LYS cc_start: 0.9118 (mtpt) cc_final: 0.8817 (mtmm)
REVERT: A  747 GLU cc_start: 0.7743 (mp0) cc_final: 0.7462 (mp0)
REVERT: A  769 MET cc_start: 0.6707 (ppp) cc_final: 0.6349 (ppp)
REVERT: B  163 TYR cc_start: 0.7490 (p90) cc_final: 0.6689 (p90)
  outliers start: 14
  outliers final: 7
  residues processed: 145
  average time/residue: 0.0827
  time to fit residues: 19.0265
Evaluate side-chains
  122 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 115
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  225 TYR
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  419 ILE
Chi-restraints excluded: chain A residue  510 HIS
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  692 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 96 optimal weight:    0.0040
   chunk 31 optimal weight:    0.3980
   chunk 114 optimal weight:    7.9990
   chunk 22 optimal weight:    4.9990
   chunk 3 optimal weight:    8.9990
   chunk 68 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 91 optimal weight:    6.9990
   chunk 127 optimal weight:    3.9990
   chunk 60 optimal weight:    9.9990
   overall best weight:    1.4796

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

Flipped N/Q/H residues before XYZ refinement:
** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 547 ASN
** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.097475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.069592 restraints weight = 40880.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.071705 restraints weight = 21498.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.073071 restraints weight = 14574.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.073867 restraints weight = 11511.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.074172 restraints weight = 10111.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11734  Z= 0.131
  Angle     :  0.666   9.497  15892  Z= 0.335
  Chirality :  0.043   0.163   1759
  Planarity :  0.004   0.038   2010
  Dihedral  : 11.037 165.416   1605
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.10 %
    Favored  : 88.90 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 13.85 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.62 (0.22), residues: 1406
  helix: -0.43 (0.22), residues: 557
  sheet: -1.40 (0.44), residues: 150
  loop : -3.03 (0.22), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 841 
 TYR   0.031   0.002   TYR A 476 
 PHE   0.017   0.001   PHE B 217 
 TRP   0.016   0.001   TRP A 191 
 HIS   0.006   0.001   HIS A 510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (11733)
  covalent geometry    : angle       0.66650 (15890)
  SS BOND              : bond        0.00334 (    1)
  SS BOND              : angle       0.25307 (    2)
  hydrogen bonds       : bond        0.04295 (  424)
  hydrogen bonds       : angle       5.58959 ( 1200)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 LEU cc_start: 0.8884 (tt) cc_final: 0.8547 (tt)
REVERT: A  538 MET cc_start: 0.8120 (mpp) cc_final: 0.7557 (mpp)
REVERT: A  747 GLU cc_start: 0.7712 (mp0) cc_final: 0.7476 (mp0)
REVERT: A  875 MET cc_start: 0.8536 (tmm) cc_final: 0.8046 (ppp)
REVERT: A 1138 ASN cc_start: 0.7899 (t0) cc_final: 0.7651 (t0)
REVERT: B   40 ARG cc_start: 0.8058 (ptp90) cc_final: 0.7729 (ptt90)
REVERT: B  163 TYR cc_start: 0.7855 (p90) cc_final: 0.6977 (p90)
  outliers start: 20
  outliers final: 12
  residues processed: 148
  average time/residue: 0.0778
  time to fit residues: 18.4094
Evaluate side-chains
  135 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  225 TYR
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  403 SER
Chi-restraints excluded: chain A residue  510 HIS
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue 1026 LEU
Chi-restraints excluded: chain A residue 1160 VAL
Chi-restraints excluded: chain B residue  124 TYR
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  342 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 45 optimal weight:   10.0000
   chunk 58 optimal weight:    9.9990
   chunk 127 optimal weight:    0.9990
   chunk 92 optimal weight:    0.0970
   chunk 105 optimal weight:    6.9990
   chunk 24 optimal weight:   10.0000
   chunk 1 optimal weight:    7.9990
   chunk 47 optimal weight:   10.0000
   chunk 41 optimal weight:    0.7980
   chunk 136 optimal weight:    9.9990
   chunk 100 optimal weight:    8.9990
   overall best weight:    3.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 415 GLN
A 474 GLN
** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 917 GLN
** A 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 147 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.096243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.068164 restraints weight = 41036.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.070165 restraints weight = 22272.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.071428 restraints weight = 15352.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.072089 restraints weight = 12330.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.072639 restraints weight = 10997.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11734  Z= 0.178
  Angle     :  0.690   8.666  15892  Z= 0.350
  Chirality :  0.044   0.164   1759
  Planarity :  0.004   0.066   2010
  Dihedral  : 10.675 156.928   1602
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 14.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.31 %
    Favored  : 88.69 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 17.39 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.52 (0.22), residues: 1406
  helix: -0.38 (0.22), residues: 551
  sheet: -1.33 (0.45), residues: 147
  loop : -2.92 (0.23), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 841 
 TYR   0.030   0.002   TYR A 476 
 PHE   0.029   0.002   PHE A 529 
 TRP   0.016   0.001   TRP A 191 
 HIS   0.005   0.001   HIS A 510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (11733)
  covalent geometry    : angle       0.68953 (15890)
  SS BOND              : bond        0.00252 (    1)
  SS BOND              : angle       1.10091 (    2)
  hydrogen bonds       : bond        0.04562 (  424)
  hydrogen bonds       : angle       5.62844 ( 1200)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 121
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 LEU cc_start: 0.8926 (tt) cc_final: 0.8568 (tt)
REVERT: A  538 MET cc_start: 0.8148 (mpp) cc_final: 0.7559 (mpp)
REVERT: A  747 GLU cc_start: 0.7783 (mp0) cc_final: 0.7528 (mp0)
REVERT: B   56 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7787 (mp)
REVERT: B  163 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7205 (p90)
  outliers start: 28
  outliers final: 18
  residues processed: 136
  average time/residue: 0.0731
  time to fit residues: 16.2622
Evaluate side-chains
  136 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  403 SER
Chi-restraints excluded: chain A residue  510 HIS
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  880 VAL
Chi-restraints excluded: chain A residue 1011 LEU
Chi-restraints excluded: chain A residue 1026 LEU
Chi-restraints excluded: chain A residue 1160 VAL
Chi-restraints excluded: chain A residue 1167 SER
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  163 TYR
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  342 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 126 optimal weight:    9.9990
   chunk 131 optimal weight:    2.9990
   chunk 132 optimal weight:    1.9990
   chunk 25 optimal weight:    9.9990
   chunk 89 optimal weight:    0.9980
   chunk 82 optimal weight:    5.9990
   chunk 87 optimal weight:    7.9990
   chunk 110 optimal weight:   20.0000
   chunk 36 optimal weight:   10.0000
   chunk 86 optimal weight:    0.9980
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 545 GLN
** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.097196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.069129 restraints weight = 40708.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.071153 restraints weight = 22161.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.072439 restraints weight = 15389.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.073191 restraints weight = 12397.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.073492 restraints weight = 10961.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11734  Z= 0.139
  Angle     :  0.668  10.005  15892  Z= 0.335
  Chirality :  0.043   0.149   1759
  Planarity :  0.004   0.044   2010
  Dihedral  : 10.294 153.155   1602
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.74 %
    Favored  : 89.26 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 18.68 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.35 (0.22), residues: 1406
  helix: -0.29 (0.22), residues: 554
  sheet: -1.26 (0.44), residues: 154
  loop : -2.79 (0.23), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 841 
 TYR   0.038   0.002   TYR A 476 
 PHE   0.023   0.001   PHE A 529 
 TRP   0.015   0.001   TRP A 191 
 HIS   0.005   0.001   HIS A 510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (11733)
  covalent geometry    : angle       0.66791 (15890)
  SS BOND              : bond        0.00396 (    1)
  SS BOND              : angle       0.37210 (    2)
  hydrogen bonds       : bond        0.04258 (  424)
  hydrogen bonds       : angle       5.47449 ( 1200)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 129
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 LEU cc_start: 0.8904 (tt) cc_final: 0.8540 (tt)
REVERT: A  538 MET cc_start: 0.8164 (mpp) cc_final: 0.7532 (mpp)
REVERT: A  747 GLU cc_start: 0.7815 (mp0) cc_final: 0.7568 (mp0)
REVERT: A  875 MET cc_start: 0.8776 (ppp) cc_final: 0.8563 (ppp)
REVERT: B   40 ARG cc_start: 0.8020 (ptp90) cc_final: 0.7717 (ptt90)
REVERT: B   56 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7667 (mp)
REVERT: B  163 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.7218 (p90)
  outliers start: 33
  outliers final: 21
  residues processed: 150
  average time/residue: 0.0743
  time to fit residues: 17.9698
Evaluate side-chains
  146 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  419 ILE
Chi-restraints excluded: chain A residue  510 HIS
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue 1026 LEU
Chi-restraints excluded: chain A residue 1160 VAL
Chi-restraints excluded: chain A residue 1167 SER
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  124 TYR
Chi-restraints excluded: chain B residue  163 TYR
Chi-restraints excluded: chain B residue  182 PHE
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  342 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 53 optimal weight:   20.0000
   chunk 117 optimal weight:   10.0000
   chunk 44 optimal weight:   20.0000
   chunk 70 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   chunk 52 optimal weight:    9.9990
   chunk 64 optimal weight:    2.9990
   chunk 50 optimal weight:    7.9990
   chunk 131 optimal weight:    0.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
A 545 GLN
** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.097103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.072145 restraints weight = 41212.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.072077 restraints weight = 32474.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.072353 restraints weight = 23044.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.072712 restraints weight = 21477.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.072755 restraints weight = 19659.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.2376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11734  Z= 0.137
  Angle     :  0.672  12.363  15892  Z= 0.333
  Chirality :  0.043   0.158   1759
  Planarity :  0.004   0.040   2010
  Dihedral  :  9.919 144.884   1602
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.10 %
    Favored  : 88.90 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 20.37 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.25 (0.23), residues: 1406
  helix: -0.20 (0.22), residues: 554
  sheet: -1.24 (0.44), residues: 154
  loop : -2.72 (0.23), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 600 
 TYR   0.036   0.002   TYR A 476 
 PHE   0.019   0.001   PHE A 529 
 TRP   0.014   0.001   TRP A 191 
 HIS   0.005   0.001   HIS A 510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (11733)
  covalent geometry    : angle       0.67187 (15890)
  SS BOND              : bond        0.00373 (    1)
  SS BOND              : angle       0.33846 (    2)
  hydrogen bonds       : bond        0.04130 (  424)
  hydrogen bonds       : angle       5.36319 ( 1200)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 130
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 LEU cc_start: 0.8879 (tt) cc_final: 0.8489 (tt)
REVERT: A  538 MET cc_start: 0.8121 (mpp) cc_final: 0.7739 (mpp)
REVERT: A  747 GLU cc_start: 0.7796 (mp0) cc_final: 0.7555 (mp0)
REVERT: A  875 MET cc_start: 0.8800 (ppp) cc_final: 0.8551 (ppp)
REVERT: B   40 ARG cc_start: 0.8020 (ptp90) cc_final: 0.7776 (ptt90)
REVERT: B   56 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7695 (mp)
REVERT: B  163 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.7074 (p90)
  outliers start: 31
  outliers final: 24
  residues processed: 148
  average time/residue: 0.0746
  time to fit residues: 17.7788
Evaluate side-chains
  149 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 123
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 PHE
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  419 ILE
Chi-restraints excluded: chain A residue  510 HIS
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  657 CYS
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  880 VAL
Chi-restraints excluded: chain A residue 1026 LEU
Chi-restraints excluded: chain A residue 1160 VAL
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  163 TYR
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  182 PHE
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  342 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 107 optimal weight:    7.9990
   chunk 70 optimal weight:    0.9990
   chunk 61 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 41 optimal weight:    0.4980
   chunk 40 optimal weight:    5.9990
   chunk 52 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 50 optimal weight:    6.9990
   chunk 88 optimal weight:    6.9990
   chunk 109 optimal weight:    4.9990
   overall best weight:    3.6988

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.096127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.068082 restraints weight = 40826.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.070034 restraints weight = 22470.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.071246 restraints weight = 15620.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.072047 restraints weight = 12629.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.072310 restraints weight = 11100.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11734  Z= 0.187
  Angle     :  0.712  13.971  15892  Z= 0.354
  Chirality :  0.044   0.154   1759
  Planarity :  0.004   0.042   2010
  Dihedral  :  9.906 139.347   1602
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.59 %
    Favored  : 88.41 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 20.93 %
    Favored  : 76.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.37 (0.23), residues: 1406
  helix: -0.29 (0.22), residues: 562
  sheet: -1.29 (0.44), residues: 154
  loop : -2.82 (0.23), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 631 
 TYR   0.032   0.002   TYR A 476 
 PHE   0.020   0.002   PHE B 217 
 TRP   0.015   0.001   TRP A 191 
 HIS   0.005   0.001   HIS A 510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 (11733)
  covalent geometry    : angle       0.71164 (15890)
  SS BOND              : bond        0.00331 (    1)
  SS BOND              : angle       0.27924 (    2)
  hydrogen bonds       : bond        0.04523 (  424)
  hydrogen bonds       : angle       5.49692 ( 1200)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 120
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: A  538 MET cc_start: 0.8291 (mpp) cc_final: 0.7657 (mpp)
REVERT: A  747 GLU cc_start: 0.7890 (mp0) cc_final: 0.7595 (mp0)
REVERT: A  875 MET cc_start: 0.8840 (ppp) cc_final: 0.8574 (ppp)
REVERT: B   56 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7720 (mp)
REVERT: B  163 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7082 (p90)
  outliers start: 33
  outliers final: 28
  residues processed: 141
  average time/residue: 0.0715
  time to fit residues: 16.5149
Evaluate side-chains
  147 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 117
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 PHE
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  474 GLN
Chi-restraints excluded: chain A residue  510 HIS
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  657 CYS
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  880 VAL
Chi-restraints excluded: chain A residue 1008 SER
Chi-restraints excluded: chain A residue 1026 LEU
Chi-restraints excluded: chain A residue 1160 VAL
Chi-restraints excluded: chain A residue 1167 SER
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  124 TYR
Chi-restraints excluded: chain B residue  163 TYR
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  182 PHE
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  342 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 69 optimal weight:    9.9990
   chunk 36 optimal weight:    7.9990
   chunk 62 optimal weight:   10.0000
   chunk 59 optimal weight:    9.9990
   chunk 1 optimal weight:   20.0000
   chunk 107 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 49 optimal weight:    9.9990
   chunk 44 optimal weight:    0.2980
   chunk 11 optimal weight:   10.0000
   overall best weight:    3.6588

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  45 GLN
** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.096078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.067750 restraints weight = 40854.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.069737 restraints weight = 22138.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.071000 restraints weight = 15376.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.071738 restraints weight = 12384.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.071739 restraints weight = 10941.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  11734  Z= 0.185
  Angle     :  0.720  14.077  15892  Z= 0.355
  Chirality :  0.044   0.150   1759
  Planarity :  0.004   0.043   2010
  Dihedral  :  9.841 137.988   1602
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.74 %
    Favored  : 88.26 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 21.34 %
    Favored  : 75.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.35 (0.23), residues: 1406
  helix: -0.29 (0.22), residues: 563
  sheet: -1.31 (0.44), residues: 155
  loop : -2.80 (0.23), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 229 
 TYR   0.035   0.002   TYR A 476 
 PHE   0.020   0.002   PHE B 217 
 TRP   0.014   0.001   TRP A 805 
 HIS   0.005   0.001   HIS A 510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 (11733)
  covalent geometry    : angle       0.72038 (15890)
  SS BOND              : bond        0.00311 (    1)
  SS BOND              : angle       0.28436 (    2)
  hydrogen bonds       : bond        0.04479 (  424)
  hydrogen bonds       : angle       5.51212 ( 1200)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 122
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 LEU cc_start: 0.8878 (tt) cc_final: 0.8655 (tt)
REVERT: A  538 MET cc_start: 0.8268 (mpp) cc_final: 0.7628 (mpp)
REVERT: A  747 GLU cc_start: 0.7902 (mp0) cc_final: 0.7597 (mp0)
REVERT: A  875 MET cc_start: 0.8888 (ppp) cc_final: 0.8590 (ppp)
REVERT: B   56 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7717 (mp)
REVERT: B  163 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7114 (p90)
  outliers start: 38
  outliers final: 34
  residues processed: 146
  average time/residue: 0.0672
  time to fit residues: 16.2867
Evaluate side-chains
  153 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 117
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 PHE
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain A residue  349 ILE
Chi-restraints excluded: chain A residue  392 TYR
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  403 SER
Chi-restraints excluded: chain A residue  419 ILE
Chi-restraints excluded: chain A residue  474 GLN
Chi-restraints excluded: chain A residue  510 HIS
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  657 CYS
Chi-restraints excluded: chain A residue  667 THR
Chi-restraints excluded: chain A residue  880 VAL
Chi-restraints excluded: chain A residue 1008 SER
Chi-restraints excluded: chain A residue 1011 LEU
Chi-restraints excluded: chain A residue 1026 LEU
Chi-restraints excluded: chain A residue 1133 THR
Chi-restraints excluded: chain A residue 1160 VAL
Chi-restraints excluded: chain A residue 1167 SER
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  124 TYR
Chi-restraints excluded: chain B residue  163 TYR
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  182 PHE
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  342 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 90 optimal weight:    0.1980
   chunk 14 optimal weight:    1.9990
   chunk 140 optimal weight:    0.0870
   chunk 105 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9980
   chunk 74 optimal weight:   20.0000
   chunk 84 optimal weight:    0.9980
   chunk 50 optimal weight:    6.9990
   chunk 92 optimal weight:    1.9990
   chunk 115 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.6560

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
A 474 GLN
** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 965 HIS
** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.098454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.072113 restraints weight = 40445.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.072617 restraints weight = 26346.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.072766 restraints weight = 19254.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.073071 restraints weight = 18962.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.073147 restraints weight = 17904.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  11734  Z= 0.115
  Angle     :  0.687  15.229  15892  Z= 0.335
  Chirality :  0.042   0.157   1759
  Planarity :  0.004   0.039   2010
  Dihedral  :  9.478 134.746   1602
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.88 %
    Favored  : 89.12 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 22.46 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.09 (0.23), residues: 1406
  helix: -0.06 (0.22), residues: 555
  sheet: -1.17 (0.45), residues: 146
  loop : -2.63 (0.24), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 229 
 TYR   0.034   0.001   TYR A 476 
 PHE   0.021   0.001   PHE A 529 
 TRP   0.014   0.001   TRP A 805 
 HIS   0.005   0.001   HIS A 510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (11733)
  covalent geometry    : angle       0.68703 (15890)
  SS BOND              : bond        0.00344 (    1)
  SS BOND              : angle       0.36465 (    2)
  hydrogen bonds       : bond        0.03843 (  424)
  hydrogen bonds       : angle       5.26670 ( 1200)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 135
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A  130 LEU cc_start: 0.8722 (tt) cc_final: 0.8487 (tt)
REVERT: A  412 ARG cc_start: 0.7860 (mtt-85) cc_final: 0.7627 (mtt-85)
REVERT: A  538 MET cc_start: 0.8219 (mpp) cc_final: 0.7662 (mpp)
REVERT: A  747 GLU cc_start: 0.7803 (mp0) cc_final: 0.7517 (mp0)
REVERT: A  875 MET cc_start: 0.8786 (ppp) cc_final: 0.8579 (ppp)
REVERT: A 1000 MET cc_start: 0.8610 (tmm) cc_final: 0.8333 (tmm)
REVERT: B   40 ARG cc_start: 0.7968 (ptp90) cc_final: 0.7729 (ptt90)
REVERT: B   56 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7704 (mp)
REVERT: B  163 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.6957 (p90)
  outliers start: 27
  outliers final: 20
  residues processed: 153
  average time/residue: 0.0788
  time to fit residues: 19.0519
Evaluate side-chains
  148 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 PHE
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  392 TYR
Chi-restraints excluded: chain A residue  419 ILE
Chi-restraints excluded: chain A residue  474 GLN
Chi-restraints excluded: chain A residue  510 HIS
Chi-restraints excluded: chain A residue  657 CYS
Chi-restraints excluded: chain A residue 1008 SER
Chi-restraints excluded: chain A residue 1026 LEU
Chi-restraints excluded: chain A residue 1160 VAL
Chi-restraints excluded: chain A residue 1167 SER
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  124 TYR
Chi-restraints excluded: chain B residue  163 TYR
Chi-restraints excluded: chain B residue  182 PHE
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  304 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 137 optimal weight:    0.0870
   chunk 101 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 38 optimal weight:    7.9990
   chunk 16 optimal weight:   10.0000
   chunk 40 optimal weight:    3.9990
   chunk 108 optimal weight:    0.7980
   chunk 54 optimal weight:    9.9990
   chunk 86 optimal weight:    5.9990
   chunk 111 optimal weight:    0.5980
   chunk 67 optimal weight:    0.7980
   overall best weight:    1.0560

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.098590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.070975 restraints weight = 40823.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.072905 restraints weight = 22847.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.074134 restraints weight = 16257.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.074753 restraints weight = 13245.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.075264 restraints weight = 11892.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.2876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11734  Z= 0.116
  Angle     :  0.690  15.230  15892  Z= 0.334
  Chirality :  0.042   0.155   1759
  Planarity :  0.004   0.039   2010
  Dihedral  :  9.262 129.104   1602
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.88 %
    Favored  : 89.12 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 23.03 %
    Favored  : 74.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.90 (0.23), residues: 1406
  helix:  0.10 (0.23), residues: 541
  sheet: -1.15 (0.44), residues: 153
  loop : -2.45 (0.24), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 628 
 TYR   0.025   0.001   TYR A 476 
 PHE   0.022   0.001   PHE B 340 
 TRP   0.013   0.001   TRP A 191 
 HIS   0.005   0.001   HIS A 630 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (11733)
  covalent geometry    : angle       0.68965 (15890)
  SS BOND              : bond        0.00346 (    1)
  SS BOND              : angle       0.34269 (    2)
  hydrogen bonds       : bond        0.03736 (  424)
  hydrogen bonds       : angle       5.21015 ( 1200)

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

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

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2812 Ramachandran restraints generated.
    1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 132
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 LEU cc_start: 0.8722 (tt) cc_final: 0.8457 (tt)
REVERT: A  412 ARG cc_start: 0.7883 (mtt-85) cc_final: 0.7657 (mtt-85)
REVERT: A  538 MET cc_start: 0.8203 (mpp) cc_final: 0.7625 (mpp)
REVERT: A  747 GLU cc_start: 0.7752 (mp0) cc_final: 0.7471 (mp0)
REVERT: A  875 MET cc_start: 0.8808 (ppp) cc_final: 0.8570 (ppp)
REVERT: A  879 LEU cc_start: 0.9202 (mt) cc_final: 0.8863 (tp)
REVERT: A 1000 MET cc_start: 0.8582 (tmm) cc_final: 0.8303 (tmm)
REVERT: B   56 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7670 (mp)
REVERT: B  163 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.6884 (p90)
  outliers start: 25
  outliers final: 19
  residues processed: 149
  average time/residue: 0.0749
  time to fit residues: 17.4079
Evaluate side-chains
  149 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 PHE
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  392 TYR
Chi-restraints excluded: chain A residue  419 ILE
Chi-restraints excluded: chain A residue  510 HIS
Chi-restraints excluded: chain A residue  657 CYS
Chi-restraints excluded: chain A residue 1008 SER
Chi-restraints excluded: chain A residue 1026 LEU
Chi-restraints excluded: chain A residue 1160 VAL
Chi-restraints excluded: chain A residue 1167 SER
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue  102 VAL
Chi-restraints excluded: chain B residue  124 TYR
Chi-restraints excluded: chain B residue  163 TYR
Chi-restraints excluded: chain B residue  182 PHE
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  304 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 99 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   chunk 120 optimal weight:   20.0000
   chunk 108 optimal weight:    5.9990
   chunk 72 optimal weight:   20.0000
   chunk 7 optimal weight:    6.9990
   chunk 134 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 137 optimal weight:    0.1980
   chunk 15 optimal weight:    2.9990
   overall best weight:    2.6386

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

Flipped N/Q/H residues before XYZ refinement:
** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.097348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.071738 restraints weight = 41205.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.071905 restraints weight = 28474.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.072184 restraints weight = 20841.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.072467 restraints weight = 19849.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.072473 restraints weight = 18611.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.2814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11734  Z= 0.150
  Angle     :  0.708  14.649  15892  Z= 0.345
  Chirality :  0.043   0.167   1759
  Planarity :  0.004   0.040   2010
  Dihedral  :  9.224 125.502   1602
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 14.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.74 %
    Favored  : 89.26 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 23.43 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.95 (0.23), residues: 1406
  helix: -0.01 (0.23), residues: 554
  sheet: -1.12 (0.43), residues: 160
  loop : -2.49 (0.24), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 841 
 TYR   0.029   0.002   TYR A 476 
 PHE   0.018   0.001   PHE B 217 
 TRP   0.013   0.001   TRP A 191 
 HIS   0.004   0.001   HIS A 510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (11733)
  covalent geometry    : angle       0.70782 (15890)
  SS BOND              : bond        0.00300 (    1)
  SS BOND              : angle       0.29054 (    2)
  hydrogen bonds       : bond        0.04045 (  424)
  hydrogen bonds       : angle       5.29959 ( 1200)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1734.42 seconds
wall clock time: 31 minutes 5.50 seconds (1865.50 seconds total)