Starting phenix.real_space_refine
on Sun May 11 04:47:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yg4_33807/05_2025/7yg4_33807.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yg4_33807/05_2025/7yg4_33807.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yg4_33807/05_2025/7yg4_33807.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yg4_33807/05_2025/7yg4_33807.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yg4_33807/05_2025/7yg4_33807.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yg4_33807/05_2025/7yg4_33807.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.048
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    4779      2.51       5
     N    1270      2.21       5
     O    1421      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7510
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6432
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 819, 6432
          Classifications: {'peptide': 819}
          Link IDs: {'PTRANS': 27, 'TRANS': 791}
          Chain breaks: 7
    Chain: "B"
      Number of atoms: 539
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 67, 539
          Classifications: {'peptide': 67}
          Link IDs: {'TRANS': 66}
    Chain: "E"
      Number of atoms: 539
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 67, 539
          Classifications: {'peptide': 67}
          Link IDs: {'TRANS': 66}
  Time building chain proxies: 4.30, per 1000 atoms: 0.57
  Number of scatterers: 7510
  At special positions: 0
  Unit cell: (91.8, 113.05, 142.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      40     16.00
     O    1421      8.00
     N    1270      7.00
     C    4779      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.63
  Conformation dependent library (CDL) restraints added in 926.8 milliseconds
  

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1822

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 0 sheets defined
      82.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 381 through 392
    Processing helix  chain 'A' and resid 397 through 413
      Proline residue:  A 408  - end of helix
      removed outlier: 3.882A  pdb=" N   ILE A 412 " --> pdb=" O   PRO A 408 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   LYS A 413 " --> pdb=" O   SER A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 439
    Processing helix  chain 'A' and resid 440 through 445
    Processing helix  chain 'A' and resid 452 through 458
      removed outlier: 3.799A  pdb=" N   LEU A 456 " --> pdb=" O   ASN A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 470
      removed outlier: 4.240A  pdb=" N   GLU A 468 " --> pdb=" O   SER A 464 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   CYS A 469 " --> pdb=" O   SER A 465 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   GLY A 470 " --> pdb=" O   LEU A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 481
      removed outlier: 3.688A  pdb=" N   GLY A 476 " --> pdb=" O   GLN A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 486
    Processing helix  chain 'A' and resid 486 through 491
      removed outlier: 3.893A  pdb=" N   LEU A 490 " --> pdb=" O   LEU A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 509
      removed outlier: 3.636A  pdb=" N   ASN A 502 " --> pdb=" O   SER A 498 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   LYS A 505 " --> pdb=" O   LEU A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 522
      removed outlier: 3.864A  pdb=" N   ALA A 519 " --> pdb=" O   GLU A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 540
      removed outlier: 3.606A  pdb=" N   LEU A 539 " --> pdb=" O   LEU A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 575
      removed outlier: 3.516A  pdb=" N   THR A 548 " --> pdb=" O   VAL A 544 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   SER A 551 " --> pdb=" O   VAL A 547 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ILE A 553 " --> pdb=" O   ALA A 549 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   TYR A 560 " --> pdb=" O   LYS A 556 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLU A 565 " --> pdb=" O   GLU A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 640
      removed outlier: 4.740A  pdb=" N   ARG A 626 " --> pdb=" O   GLY A 622 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LEU A 627 " --> pdb=" O   GLU A 623 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLU A 633 " --> pdb=" O   ASN A 629 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   PHE A 635 " --> pdb=" O   LEU A 631 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLU A 639 " --> pdb=" O   PHE A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 645
    Processing helix  chain 'A' and resid 668 through 679
    Processing helix  chain 'A' and resid 681 through 689
      removed outlier: 4.095A  pdb=" N   LEU A 687 " --> pdb=" O   GLU A 683 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 712
      removed outlier: 3.833A  pdb=" N   VAL A 707 " --> pdb=" O   ALA A 703 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU A 708 " --> pdb=" O   THR A 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 714 through 724
      removed outlier: 3.523A  pdb=" N   MET A 722 " --> pdb=" O   LEU A 718 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   GLU A 724 " --> pdb=" O   PHE A 720 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 724 through 737
      removed outlier: 3.596A  pdb=" N   ASN A 729 " --> pdb=" O   TYR A 725 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU A 730 " --> pdb=" O   GLU A 726 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 756 through 781
      removed outlier: 3.608A  pdb=" N   PHE A 778 " --> pdb=" O   LEU A 774 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLN A 779 " --> pdb=" O   PHE A 775 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 789 through 803
      removed outlier: 3.571A  pdb=" N   THR A 803 " --> pdb=" O   LEU A 799 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 805 through 816
      removed outlier: 3.747A  pdb=" N   ALA A 811 " --> pdb=" O   VAL A 807 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   HIS A 814 " --> pdb=" O   SER A 810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 832
      removed outlier: 3.602A  pdb=" N   ILE A 826 " --> pdb=" O   LEU A 822 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   TYR A 832 " --> pdb=" O   LEU A 828 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 845 through 862
      removed outlier: 3.622A  pdb=" N   ASN A 849 " --> pdb=" O   SER A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 867 through 882
      removed outlier: 3.547A  pdb=" N   ALA A 872 " --> pdb=" O   LEU A 868 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   ALA A 873 " --> pdb=" O   GLU A 869 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   SER A 874 " --> pdb=" O   GLN A 870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 887 through 895
      removed outlier: 3.716A  pdb=" N   LEU A 891 " --> pdb=" O   LYS A 887 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   LYS A 893 " --> pdb=" O   GLN A 889 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU A 895 " --> pdb=" O   LEU A 891 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 904 through 906
      No H-bonds generated for 'chain 'A' and resid 904 through 906'
    Processing helix  chain 'A' and resid 907 through 918
    Processing helix  chain 'A' and resid 929 through 941
      removed outlier: 3.614A  pdb=" N   LEU A 937 " --> pdb=" O   ALA A 933 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ASN A 939 " --> pdb=" O   ARG A 935 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ALA A 941 " --> pdb=" O   LEU A 937 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 966
      removed outlier: 3.649A  pdb=" N   LEU A 958 " --> pdb=" O   LEU A 954 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 967 through 984
      removed outlier: 3.590A  pdb=" N   ILE A 982 " --> pdb=" O   LYS A 978 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU A 983 " --> pdb=" O   LEU A 979 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   THR A 984 " --> pdb=" O   ASN A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 985 through 990
      removed outlier: 3.799A  pdb=" N   ARG A 988 " --> pdb=" O   GLN A 985 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LEU A 989 " --> pdb=" O   PRO A 986 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 995 through 1021
      removed outlier: 3.860A  pdb=" N   ARG A 999 " --> pdb=" O   THR A 995 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLU A1019 " --> pdb=" O   THR A1015 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1032 through 1044
      removed outlier: 3.524A  pdb=" N   LEU A1037 " --> pdb=" O   VAL A1033 " (cutoff:3.500A)
      removed outlier: 5.820A  pdb=" N   VAL A1038 " --> pdb=" O   PRO A1034 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   THR A1039 " --> pdb=" O   SER A1035 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1056 through 1074
      removed outlier: 3.658A  pdb=" N   ILE A1060 " --> pdb=" O   ASP A1056 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   GLN A1061 " --> pdb=" O   GLU A1057 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   PHE A1071 " --> pdb=" O   ILE A1067 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   THR A1072 " --> pdb=" O   LEU A1068 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLN A1073 " --> pdb=" O   LEU A1069 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLY A1074 " --> pdb=" O   THR A1070 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1082 through 1088
    Processing helix  chain 'A' and resid 1089 through 1103
    Processing helix  chain 'A' and resid 1109 through 1120
    Processing helix  chain 'A' and resid 1138 through 1154
      removed outlier: 4.067A  pdb=" N   VAL A1153 " --> pdb=" O   MET A1149 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   GLN A1154 " --> pdb=" O   HIS A1150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1154 through 1167
      removed outlier: 3.591A  pdb=" N   VAL A1162 " --> pdb=" O   LEU A1158 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   GLY A1167 " --> pdb=" O   ARG A1163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1170 through 1188
      removed outlier: 4.136A  pdb=" N   ALA A1188 " --> pdb=" O   LEU A1184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1188 through 1210
      removed outlier: 3.534A  pdb=" N   ALA A1192 " --> pdb=" O   ALA A1188 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   THR A1210 " --> pdb=" O   ASP A1206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1219 through 1234
      removed outlier: 3.585A  pdb=" N   SER A1234 " --> pdb=" O   ASP A1230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1235 through 1248
      removed outlier: 3.590A  pdb=" N   ALA A1241 " --> pdb=" O   ALA A1237 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLY A1248 " --> pdb=" O   HIS A1244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1253 through 1269
      removed outlier: 3.798A  pdb=" N   ALA A1257 " --> pdb=" O   ASP A1253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1273 through 1292
    Processing helix  chain 'B' and resid 172 through 237
      removed outlier: 4.310A  pdb=" N   LYS B 192 " --> pdb=" O   ALA B 188 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   TYR B 193 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 172 through 237
      removed outlier: 3.997A  pdb=" N   SER E 200 " --> pdb=" O   GLU E 196 " (cutoff:3.500A)

    509 hydrogen bonds defined for protein.
    1524 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: 1.90

  Time building geometry restraints manager: 1.94 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2473
        1.34 -     1.46: 1120
        1.46 -     1.58: 3958
        1.58 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 7613
  Sorted by residual:
  bond pdb=" CB  MET E 218 "
       pdb=" CG  MET E 218 "
    ideal  model  delta    sigma   weight residual
    1.520  1.477  0.043 3.00e-02 1.11e+03 2.05e+00
  bond pdb=" CB  ILE B 222 "
       pdb=" CG2 ILE B 222 "
    ideal  model  delta    sigma   weight residual
    1.521  1.477  0.044 3.30e-02 9.18e+02 1.81e+00
  bond pdb=" CB  ARG B 233 "
       pdb=" CG  ARG B 233 "
    ideal  model  delta    sigma   weight residual
    1.520  1.485  0.035 3.00e-02 1.11e+03 1.36e+00
  bond pdb=" CB  GLN B 226 "
       pdb=" CG  GLN B 226 "
    ideal  model  delta    sigma   weight residual
    1.520  1.485  0.035 3.00e-02 1.11e+03 1.34e+00
  bond pdb=" CG1 ILE A 855 "
       pdb=" CD1 ILE A 855 "
    ideal  model  delta    sigma   weight residual
    1.513  1.468  0.045 3.90e-02 6.57e+02 1.33e+00
  ... (remaining 7608 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 10175
        2.26 -     4.52: 101
        4.52 -     6.79: 14
        6.79 -     9.05: 3
        9.05 -    11.31: 1
  Bond angle restraints: 10294
  Sorted by residual:
  angle pdb=" CA  LEU E 229 "
        pdb=" CB  LEU E 229 "
        pdb=" CG  LEU E 229 "
      ideal   model   delta    sigma   weight residual
     116.30  127.61  -11.31 3.50e+00 8.16e-02 1.04e+01
  angle pdb=" C   PRO A 668 "
        pdb=" N   TYR A 669 "
        pdb=" CA  TYR A 669 "
      ideal   model   delta    sigma   weight residual
     120.09  123.97   -3.88 1.25e+00 6.40e-01 9.65e+00
  angle pdb=" N   GLN B 210 "
        pdb=" CA  GLN B 210 "
        pdb=" CB  GLN B 210 "
      ideal   model   delta    sigma   weight residual
     110.28  114.70   -4.42 1.55e+00 4.16e-01 8.13e+00
  angle pdb=" N   GLU B 216 "
        pdb=" CA  GLU B 216 "
        pdb=" CB  GLU B 216 "
      ideal   model   delta    sigma   weight residual
     110.28  114.65   -4.37 1.55e+00 4.16e-01 7.96e+00
  angle pdb=" C   VAL B 215 "
        pdb=" N   GLU B 216 "
        pdb=" CA  GLU B 216 "
      ideal   model   delta    sigma   weight residual
     120.31  116.04    4.27 1.52e+00 4.33e-01 7.90e+00
  ... (remaining 10289 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 4136
       18.00 -    35.99: 427
       35.99 -    53.99: 81
       53.99 -    71.98: 23
       71.98 -    89.98: 13
  Dihedral angle restraints: 4680
    sinusoidal: 1898
      harmonic: 2782
  Sorted by residual:
  dihedral pdb=" CA  GLU E 196 "
           pdb=" C   GLU E 196 "
           pdb=" N   LEU E 197 "
           pdb=" CA  LEU E 197 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.94   19.06     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CB  GLU A1258 "
           pdb=" CG  GLU A1258 "
           pdb=" CD  GLU A1258 "
           pdb=" OE1 GLU A1258 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.98  -89.98     1      3.00e+01 1.11e-03 1.07e+01
  dihedral pdb=" CG  ARG A 396 "
           pdb=" CD  ARG A 396 "
           pdb=" NE  ARG A 396 "
           pdb=" CZ  ARG A 396 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -134.46   44.46     2      1.50e+01 4.44e-03 1.05e+01
  ... (remaining 4677 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 945
       0.039 -    0.079: 251
       0.079 -    0.118: 43
       0.118 -    0.158: 8
       0.158 -    0.197: 2
  Chirality restraints: 1249
  Sorted by residual:
  chirality pdb=" CA  GLU E 196 "
            pdb=" N   GLU E 196 "
            pdb=" C   GLU E 196 "
            pdb=" CB  GLU E 196 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.72e-01
  chirality pdb=" CA  ILE A 691 "
            pdb=" N   ILE A 691 "
            pdb=" C   ILE A 691 "
            pdb=" CB  ILE A 691 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.38e-01
  chirality pdb=" CA  GLN B 210 "
            pdb=" N   GLN B 210 "
            pdb=" C   GLN B 210 "
            pdb=" CB  GLN B 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.96e-01
  ... (remaining 1246 not shown)

  Planarity restraints: 1296
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A1105 "    0.060 5.00e-02 4.00e+02   9.05e-02 1.31e+01
        pdb=" N   PRO A1106 "   -0.156 5.00e-02 4.00e+02
        pdb=" CA  PRO A1106 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A1106 "    0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 691 "   -0.041 5.00e-02 4.00e+02   6.28e-02 6.32e+00
        pdb=" N   PRO A 692 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 692 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 692 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B 216 "   -0.010 2.00e-02 2.50e+03   2.10e-02 4.42e+00
        pdb=" CD  GLU B 216 "    0.036 2.00e-02 2.50e+03
        pdb=" OE1 GLU B 216 "   -0.013 2.00e-02 2.50e+03
        pdb=" OE2 GLU B 216 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1293 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 119
        2.70 -     3.25: 7578
        3.25 -     3.80: 11361
        3.80 -     4.35: 14990
        4.35 -     4.90: 24770
  Nonbonded interactions: 58818
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B 198 "
            pdb=" OG  SER E 194 "
     model   vdw
     2.147 3.120
  nonbonded pdb=" O   ILE A 511 "
            pdb=" OH  TYR A 675 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" NH2 ARG B 233 "
            pdb=" OE1 GLN E 228 "
     model   vdw
     2.262 3.120
  nonbonded pdb=" O   LEU A1122 "
            pdb=" NH2 ARG A1144 "
     model   vdw
     2.268 3.120
  nonbonded pdb=" O   GLU A 883 "
            pdb=" NE2 GLN A 889 "
     model   vdw
     2.324 3.120
  ... (remaining 58813 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.220
  Find NCS groups from input model:        0.090
  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:2.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7613  Z= 0.148
  Angle     :  0.584  11.309  10294  Z= 0.307
  Chirality :  0.037   0.197   1249
  Planarity :  0.005   0.090   1296
  Dihedral  : 15.981  89.976   2858
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.28), residues: 933
  helix:  0.85 (0.20), residues: 712
  sheet:  None (None), residues: 0
  loop : -1.48 (0.38), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 760 
 HIS   0.006   0.001   HIS A 737 
 PHE   0.011   0.001   PHE A 775 
 TYR   0.010   0.001   TYR B 193 
 ARG   0.002   0.000   ARG A1163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20887 (  509)
  hydrogen bonds       : angle       6.20494 ( 1524)
  covalent geometry    : bond        0.00343 ( 7613)
  covalent geometry    : angle       0.58422 (10294)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.855 
Fit side-chains
REVERT: A  524 ARG cc_start: 0.5525 (mpp-170) cc_final: 0.5169 (mpp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.1864
  time to fit residues: 22.5996
Evaluate side-chains
  74 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 84 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A1088 ASN
** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 226 GLN
B 234 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.153315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.116570 restraints weight = 11575.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 2.58
r_work: 0.3467 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.1136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7613  Z= 0.137
  Angle     :  0.566  13.123  10294  Z= 0.286
  Chirality :  0.036   0.138   1249
  Planarity :  0.005   0.063   1296
  Dihedral  :  3.776  14.827    999
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  7.29 %
    Favored  : 92.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.27), residues: 933
  helix:  1.25 (0.19), residues: 741
  sheet:  None (None), residues: 0
  loop : -1.50 (0.40), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1091 
 HIS   0.004   0.001   HIS A 643 
 PHE   0.008   0.001   PHE A1110 
 TYR   0.014   0.001   TYR B 193 
 ARG   0.002   0.000   ARG A 935 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05433 (  509)
  hydrogen bonds       : angle       4.09333 ( 1524)
  covalent geometry    : bond        0.00299 ( 7613)
  covalent geometry    : angle       0.56552 (10294)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
REVERT: A  524 ARG cc_start: 0.5367 (mpp-170) cc_final: 0.4997 (mpp-170)
REVERT: A  725 TYR cc_start: 0.6899 (t80) cc_final: 0.6593 (t80)
REVERT: A 1001 THR cc_start: 0.7992 (m) cc_final: 0.7661 (p)
REVERT: A 1176 MET cc_start: 0.6921 (mmp) cc_final: 0.6559 (mmm)
  outliers start: 5
  outliers final: 3
  residues processed: 89
  average time/residue: 0.1786
  time to fit residues: 22.2590
Evaluate side-chains
  81 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  691 ILE
Chi-restraints excluded: chain A residue 1156 LYS
Chi-restraints excluded: chain E residue  221 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 78 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 85 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0570
   chunk 73 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 81 optimal weight:   10.0000
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
** B 190 GLN ** 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 = 0.4112 r_free = 0.4112 target = 0.154758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.116996 restraints weight = 11786.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 2.43
r_work: 0.3470 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.1432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7613  Z= 0.117
  Angle     :  0.513  11.548  10294  Z= 0.256
  Chirality :  0.035   0.128   1249
  Planarity :  0.004   0.054   1296
  Dihedral  :  3.606  14.122    999
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 10.11 %
    Favored  : 88.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.28), residues: 933
  helix:  1.61 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -1.56 (0.40), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1091 
 HIS   0.003   0.001   HIS A 643 
 PHE   0.008   0.001   PHE A1071 
 TYR   0.009   0.001   TYR B 193 
 ARG   0.002   0.000   ARG B 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04672 (  509)
  hydrogen bonds       : angle       3.73321 ( 1524)
  covalent geometry    : bond        0.00249 ( 7613)
  covalent geometry    : angle       0.51311 (10294)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
REVERT: A  475 THR cc_start: 0.8647 (m) cc_final: 0.8336 (p)
REVERT: A  524 ARG cc_start: 0.5416 (mpp-170) cc_final: 0.5032 (mpp-170)
REVERT: A 1001 THR cc_start: 0.8045 (m) cc_final: 0.7751 (p)
REVERT: B  227 GLN cc_start: 0.7995 (mt0) cc_final: 0.7639 (mt0)
  outliers start: 11
  outliers final: 4
  residues processed: 97
  average time/residue: 0.1951
  time to fit residues: 26.2455
Evaluate side-chains
  86 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  691 ILE
Chi-restraints excluded: chain A residue  737 HIS
Chi-restraints excluded: chain A residue 1156 LYS
Chi-restraints excluded: chain E residue  221 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 558 HIS
A 779 GLN
** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.152191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.114388 restraints weight = 11808.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 2.42
r_work: 0.3443 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7613  Z= 0.160
  Angle     :  0.535  11.524  10294  Z= 0.270
  Chirality :  0.037   0.142   1249
  Planarity :  0.004   0.050   1296
  Dihedral  :  3.655  14.560    999
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.05 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.28), residues: 933
  helix:  1.57 (0.19), residues: 747
  sheet:  None (None), residues: 0
  loop : -1.53 (0.42), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A1091 
 HIS   0.004   0.001   HIS A 814 
 PHE   0.014   0.001   PHE A1071 
 TYR   0.013   0.001   TYR A 560 
 ARG   0.006   0.000   ARG B 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05062 (  509)
  hydrogen bonds       : angle       3.80553 ( 1524)
  covalent geometry    : bond        0.00381 ( 7613)
  covalent geometry    : angle       0.53511 (10294)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
REVERT: A  475 THR cc_start: 0.8631 (m) cc_final: 0.8327 (p)
REVERT: A  524 ARG cc_start: 0.5510 (mpp-170) cc_final: 0.5164 (mpp-170)
REVERT: A 1001 THR cc_start: 0.8151 (m) cc_final: 0.7809 (p)
REVERT: B  228 GLN cc_start: 0.7460 (tm-30) cc_final: 0.7219 (tm-30)
  outliers start: 15
  outliers final: 10
  residues processed: 98
  average time/residue: 0.1621
  time to fit residues: 22.8887
Evaluate side-chains
  90 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  691 ILE
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  737 HIS
Chi-restraints excluded: chain A residue  906 ASN
Chi-restraints excluded: chain A residue 1015 THR
Chi-restraints excluded: chain A residue 1046 SER
Chi-restraints excluded: chain B residue  232 THR
Chi-restraints excluded: chain E residue  196 GLU
Chi-restraints excluded: chain E residue  221 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 26 optimal weight:    0.0070
   chunk 47 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0170
   chunk 32 optimal weight:    0.0970
   chunk 12 optimal weight:    0.2980
   chunk 3 optimal weight:    4.9990
   chunk 75 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 83 optimal weight:    3.9990
   overall best weight:    0.2834

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

Flipped N/Q/H residues before XYZ refinement:
** B 190 GLN ** 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 = 0.4123 r_free = 0.4123 target = 0.155852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.118478 restraints weight = 11584.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 2.39
r_work: 0.3511 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.1809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7613  Z= 0.105
  Angle     :  0.497  10.914  10294  Z= 0.249
  Chirality :  0.034   0.137   1249
  Planarity :  0.004   0.051   1296
  Dihedral  :  3.482  14.231    999
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.99 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.28), residues: 933
  helix:  1.89 (0.20), residues: 746
  sheet:  None (None), residues: 0
  loop : -1.50 (0.42), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1091 
 HIS   0.002   0.000   HIS A 643 
 PHE   0.010   0.001   PHE A1109 
 TYR   0.006   0.001   TYR B 193 
 ARG   0.004   0.000   ARG B 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03948 (  509)
  hydrogen bonds       : angle       3.54095 ( 1524)
  covalent geometry    : bond        0.00215 ( 7613)
  covalent geometry    : angle       0.49730 (10294)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.930 
Fit side-chains
REVERT: A  475 THR cc_start: 0.8635 (m) cc_final: 0.8369 (p)
REVERT: A  524 ARG cc_start: 0.5528 (mpp-170) cc_final: 0.5188 (mpp-170)
REVERT: A 1176 MET cc_start: 0.6830 (mmp) cc_final: 0.6472 (mmm)
REVERT: B  227 GLN cc_start: 0.7696 (mt0) cc_final: 0.6914 (mt0)
REVERT: B  228 GLN cc_start: 0.7389 (tm-30) cc_final: 0.7186 (tm-30)
REVERT: E  216 GLU cc_start: 0.6626 (mp0) cc_final: 0.6298 (pt0)
  outliers start: 15
  outliers final: 8
  residues processed: 95
  average time/residue: 0.1860
  time to fit residues: 24.7850
Evaluate side-chains
  88 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  691 ILE
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  737 HIS
Chi-restraints excluded: chain A residue  906 ASN
Chi-restraints excluded: chain A residue 1046 SER
Chi-restraints excluded: chain A residue 1203 ILE
Chi-restraints excluded: chain B residue  232 THR
Chi-restraints excluded: chain E residue  218 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 88 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0470
   overall best weight:    0.7280

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

Flipped N/Q/H residues before XYZ refinement:
** B 190 GLN ** 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 = 0.4118 r_free = 0.4118 target = 0.155378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.118022 restraints weight = 11584.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 2.39
r_work: 0.3487 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.1867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7613  Z= 0.116
  Angle     :  0.512  12.145  10294  Z= 0.253
  Chirality :  0.035   0.127   1249
  Planarity :  0.004   0.050   1296
  Dihedral  :  3.424  13.688    999
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 13.40 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.28), residues: 933
  helix:  1.90 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.43 (0.43), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1091 
 HIS   0.003   0.001   HIS A 814 
 PHE   0.008   0.001   PHE A1071 
 TYR   0.010   0.001   TYR A 560 
 ARG   0.005   0.000   ARG B 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04174 (  509)
  hydrogen bonds       : angle       3.52344 ( 1524)
  covalent geometry    : bond        0.00261 ( 7613)
  covalent geometry    : angle       0.51249 (10294)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
REVERT: A  475 THR cc_start: 0.8620 (m) cc_final: 0.8365 (p)
REVERT: A  524 ARG cc_start: 0.5564 (mpp-170) cc_final: 0.5226 (mpp-170)
REVERT: B  206 ASP cc_start: 0.7611 (p0) cc_final: 0.7345 (p0)
REVERT: B  210 GLN cc_start: 0.7054 (mp10) cc_final: 0.6754 (mp10)
REVERT: B  227 GLN cc_start: 0.7781 (mt0) cc_final: 0.7138 (mt0)
REVERT: E  216 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6382 (pt0)
  outliers start: 14
  outliers final: 9
  residues processed: 87
  average time/residue: 0.1862
  time to fit residues: 22.8304
Evaluate side-chains
  88 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  691 ILE
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  737 HIS
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue 1046 SER
Chi-restraints excluded: chain A residue 1203 ILE
Chi-restraints excluded: chain B residue  232 THR
Chi-restraints excluded: chain E residue  216 GLU
Chi-restraints excluded: chain E residue  221 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0870
   chunk 89 optimal weight:    0.6980
   chunk 87 optimal weight:    0.0980
   chunk 91 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 51 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** B 190 GLN ** 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 = 0.4122 r_free = 0.4122 target = 0.156084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.118491 restraints weight = 11501.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 2.41
r_work: 0.3500 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7613  Z= 0.106
  Angle     :  0.496  12.124  10294  Z= 0.247
  Chirality :  0.034   0.122   1249
  Planarity :  0.004   0.050   1296
  Dihedral  :  3.352  13.505    999
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 13.40 %
    Favored  : 85.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.28), residues: 933
  helix:  2.01 (0.19), residues: 749
  sheet:  None (None), residues: 0
  loop : -1.41 (0.43), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1091 
 HIS   0.002   0.000   HIS A 814 
 PHE   0.010   0.001   PHE A1109 
 TYR   0.008   0.001   TYR A 560 
 ARG   0.004   0.000   ARG B 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03893 (  509)
  hydrogen bonds       : angle       3.42611 ( 1524)
  covalent geometry    : bond        0.00228 ( 7613)
  covalent geometry    : angle       0.49640 (10294)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.915 
Fit side-chains
REVERT: A  475 THR cc_start: 0.8595 (m) cc_final: 0.8359 (p)
REVERT: A  524 ARG cc_start: 0.5533 (mpp-170) cc_final: 0.5193 (mpp-170)
REVERT: A  993 MET cc_start: 0.3045 (mmt) cc_final: 0.1332 (mmt)
REVERT: B  206 ASP cc_start: 0.7655 (p0) cc_final: 0.7397 (p0)
REVERT: B  227 GLN cc_start: 0.7715 (mt0) cc_final: 0.7076 (mt0)
REVERT: E  216 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.6312 (pt0)
  outliers start: 13
  outliers final: 9
  residues processed: 93
  average time/residue: 0.1856
  time to fit residues: 24.2124
Evaluate side-chains
  88 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  691 ILE
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  737 HIS
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  906 ASN
Chi-restraints excluded: chain A residue 1046 SER
Chi-restraints excluded: chain A residue 1203 ILE
Chi-restraints excluded: chain E residue  216 GLU
Chi-restraints excluded: chain E residue  221 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0670
   chunk 56 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   chunk 86 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
** B 190 GLN ** 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 = 0.4115 r_free = 0.4115 target = 0.155477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.118235 restraints weight = 11812.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 2.76
r_work: 0.3480 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7613  Z= 0.118
  Angle     :  0.534  13.155  10294  Z= 0.267
  Chirality :  0.035   0.190   1249
  Planarity :  0.004   0.050   1296
  Dihedral  :  3.359  13.368    999
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 13.98 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.28), residues: 933
  helix:  1.97 (0.19), residues: 749
  sheet:  None (None), residues: 0
  loop : -1.39 (0.44), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A1091 
 HIS   0.004   0.001   HIS A1175 
 PHE   0.008   0.001   PHE A1109 
 TYR   0.009   0.001   TYR A 560 
 ARG   0.005   0.000   ARG B 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04045 (  509)
  hydrogen bonds       : angle       3.48556 ( 1524)
  covalent geometry    : bond        0.00265 ( 7613)
  covalent geometry    : angle       0.53442 (10294)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.932 
Fit side-chains
REVERT: A  475 THR cc_start: 0.8627 (m) cc_final: 0.8389 (p)
REVERT: A  524 ARG cc_start: 0.5555 (mpp-170) cc_final: 0.5217 (mpp-170)
REVERT: A  993 MET cc_start: 0.3063 (mmt) cc_final: 0.1331 (mmt)
REVERT: A 1176 MET cc_start: 0.6850 (mmp) cc_final: 0.6492 (mmm)
REVERT: B  227 GLN cc_start: 0.7733 (mt0) cc_final: 0.7526 (mt0)
REVERT: B  228 GLN cc_start: 0.7340 (tm-30) cc_final: 0.7120 (tm-30)
REVERT: E  216 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6332 (pt0)
  outliers start: 13
  outliers final: 9
  residues processed: 91
  average time/residue: 0.1990
  time to fit residues: 25.1017
Evaluate side-chains
  90 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  691 ILE
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  737 HIS
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue 1046 SER
Chi-restraints excluded: chain A residue 1203 ILE
Chi-restraints excluded: chain E residue  216 GLU
Chi-restraints excluded: chain E residue  221 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 44 optimal weight:    0.4980
   chunk 1 optimal weight:    5.9990
   chunk 3 optimal weight:    0.5980
   chunk 79 optimal weight:    0.0040
   chunk 5 optimal weight:    0.5980
   chunk 85 optimal weight:    4.9990
   chunk 66 optimal weight:    0.0970
   chunk 8 optimal weight:    0.9980
   chunk 82 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.3590

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

Flipped N/Q/H residues before XYZ refinement:
** B 190 GLN ** 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 = 0.4130 r_free = 0.4130 target = 0.156910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.120043 restraints weight = 11818.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 2.71
r_work: 0.3506 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7613  Z= 0.112
  Angle     :  0.546  13.215  10294  Z= 0.280
  Chirality :  0.035   0.201   1249
  Planarity :  0.004   0.050   1296
  Dihedral  :  3.327  13.175    999
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 14.10 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.28), residues: 933
  helix:  2.00 (0.19), residues: 749
  sheet:  None (None), residues: 0
  loop : -1.38 (0.44), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1091 
 HIS   0.003   0.000   HIS A1175 
 PHE   0.008   0.001   PHE A1109 
 TYR   0.010   0.001   TYR B 193 
 ARG   0.005   0.000   ARG B 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03849 (  509)
  hydrogen bonds       : angle       3.51827 ( 1524)
  covalent geometry    : bond        0.00237 ( 7613)
  covalent geometry    : angle       0.54568 (10294)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.935 
Fit side-chains
REVERT: A  475 THR cc_start: 0.8603 (m) cc_final: 0.8384 (p)
REVERT: A  524 ARG cc_start: 0.5462 (mpp-170) cc_final: 0.5091 (mpp-170)
REVERT: A  993 MET cc_start: 0.3036 (mmt) cc_final: 0.1315 (mmt)
REVERT: A 1176 MET cc_start: 0.6851 (mmp) cc_final: 0.6463 (mmm)
REVERT: E  216 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6276 (pt0)
  outliers start: 13
  outliers final: 9
  residues processed: 90
  average time/residue: 0.1839
  time to fit residues: 23.3000
Evaluate side-chains
  89 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  691 ILE
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  737 HIS
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue 1046 SER
Chi-restraints excluded: chain A residue 1203 ILE
Chi-restraints excluded: chain E residue  216 GLU
Chi-restraints excluded: chain E residue  221 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 9 optimal weight:    0.0870
   chunk 66 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 68 optimal weight:   10.0000
   chunk 8 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.9360

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

Flipped N/Q/H residues before XYZ refinement:
** B 190 GLN ** 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 = 0.4104 r_free = 0.4104 target = 0.154798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.117528 restraints weight = 11775.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.56
r_work: 0.3480 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7613  Z= 0.134
  Angle     :  0.574  13.423  10294  Z= 0.293
  Chirality :  0.037   0.196   1249
  Planarity :  0.004   0.049   1296
  Dihedral  :  3.383  13.058    999
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 14.34 %
    Favored  : 84.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.28), residues: 933
  helix:  1.84 (0.19), residues: 749
  sheet:  None (None), residues: 0
  loop : -1.42 (0.44), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A1091 
 HIS   0.003   0.001   HIS A 814 
 PHE   0.008   0.001   PHE A1071 
 TYR   0.012   0.001   TYR A 560 
 ARG   0.005   0.000   ARG B 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04335 (  509)
  hydrogen bonds       : angle       3.64570 ( 1524)
  covalent geometry    : bond        0.00311 ( 7613)
  covalent geometry    : angle       0.57386 (10294)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
REVERT: A  475 THR cc_start: 0.8640 (m) cc_final: 0.8395 (p)
REVERT: A  524 ARG cc_start: 0.5536 (mpp-170) cc_final: 0.5165 (mpp-170)
REVERT: A  993 MET cc_start: 0.3011 (mmt) cc_final: 0.1261 (mmt)
REVERT: A 1176 MET cc_start: 0.6921 (mmp) cc_final: 0.6534 (mmm)
  outliers start: 12
  outliers final: 10
  residues processed: 84
  average time/residue: 0.1835
  time to fit residues: 21.5794
Evaluate side-chains
  86 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  684 LEU
Chi-restraints excluded: chain A residue  691 ILE
Chi-restraints excluded: chain A residue  693 VAL
Chi-restraints excluded: chain A residue  737 HIS
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue 1046 SER
Chi-restraints excluded: chain A residue 1203 ILE
Chi-restraints excluded: chain E residue  216 GLU
Chi-restraints excluded: chain E residue  221 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 82 optimal weight:    9.9990
   chunk 34 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 80 optimal weight:    9.9990
   chunk 53 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0980
   chunk 49 optimal weight:    0.0970
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 219 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.153797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.116481 restraints weight = 11795.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3624 rms_B_bonded: 2.59
r_work: 0.3459 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7613  Z= 0.139
  Angle     :  0.574  13.269  10294  Z= 0.292
  Chirality :  0.037   0.189   1249
  Planarity :  0.004   0.049   1296
  Dihedral  :  3.448  13.292    999
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 14.69 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.28), residues: 933
  helix:  1.76 (0.19), residues: 749
  sheet:  None (None), residues: 0
  loop : -1.44 (0.44), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A1091 
 HIS   0.003   0.001   HIS A 814 
 PHE   0.009   0.001   PHE A1109 
 TYR   0.012   0.001   TYR A 560 
 ARG   0.006   0.000   ARG A1197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04513 (  509)
  hydrogen bonds       : angle       3.70195 ( 1524)
  covalent geometry    : bond        0.00323 ( 7613)
  covalent geometry    : angle       0.57402 (10294)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3817.04 seconds
wall clock time: 66 minutes 50.34 seconds (4010.34 seconds total)