Starting phenix.real_space_refine
on Wed Mar  4 05:35:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nj1_12369/03_2026/7nj1_12369.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nj1_12369/03_2026/7nj1_12369.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nj1_12369/03_2026/7nj1_12369.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nj1_12369/03_2026/7nj1_12369.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nj1_12369/03_2026/7nj1_12369.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nj1_12369/03_2026/7nj1_12369.map"
  }
  resolution = 2.9
  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=   0.001 sd=   0.017
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      52      5.16       5
     C    7043      2.51       5
     N    1944      2.21       5
     O    2057      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 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: 11096
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10660
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1448, 10660
          Classifications: {'peptide': 1448}
          Incomplete info: {'truncation_to_alanine': 175}
          Link IDs: {'PTRANS': 67, 'TRANS': 1380}
          Chain breaks: 5
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 634
          Unresolved non-hydrogen angles: 808
          Unresolved non-hydrogen dihedrals: 531
          Unresolved non-hydrogen chiralities: 57
          Planarities with less than four sites: {'GLU:plan': 10, 'HIS:plan': 5, 'ARG:plan': 11, 'PHE:plan': 9, 'TRP:plan': 2, 'ASP:plan': 10, 'TYR:plan': 8, 'ASN:plan1': 2, 'GLN:plan1': 17}
          Unresolved non-hydrogen planarities: 352
    Chain: "B"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 436
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 45}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
  Time building chain proxies: 2.41, per 1000 atoms: 0.22
  Number of scatterers: 11096
  At special positions: 0
  Unit cell: (89.25, 89.25, 185.85, 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      52     16.00
     O    2057      8.00
     N    1944      7.00
     C    7043      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 637 " - pdb=" SG  CYS A 687 " distance=2.04

  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: 0.76
  Conformation dependent library (CDL) restraints added in 551.4 milliseconds
  

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2838

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 2 sheets defined
      69.7% alpha, 2.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 251 through 263
      removed outlier: 3.759A  pdb=" N   THR A 255 " --> pdb=" O   LEU A 251 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   GLU A 257 " --> pdb=" O   GLU A 253 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   HIS A 258 " --> pdb=" O   LEU A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 271
    Processing helix  chain 'A' and resid 277 through 291
      removed outlier: 3.518A  pdb=" N   THR A 285 " --> pdb=" O   TYR A 281 " (cutoff:3.500A)
      Proline residue:  A 289  - end of helix
    Processing helix  chain 'A' and resid 298 through 302
    Processing helix  chain 'A' and resid 312 through 320
      removed outlier: 3.633A  pdb=" N   ILE A 316 " --> pdb=" O   ALA A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 346
      removed outlier: 4.012A  pdb=" N   LEU A 333 " --> pdb=" O   PRO A 329 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   SER A 345 " --> pdb=" O   GLN A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 367
    Processing helix  chain 'A' and resid 376 through 390
      removed outlier: 4.057A  pdb=" N   ASP A 380 " --> pdb=" O   GLN A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 393
      No H-bonds generated for 'chain 'A' and resid 391 through 393'
    Processing helix  chain 'A' and resid 400 through 418
      removed outlier: 3.642A  pdb=" N   VAL A 406 " --> pdb=" O   HIS A 402 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   VAL A 408 " --> pdb=" O   TYR A 404 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   TYR A 409 " --> pdb=" O   THR A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 442
      removed outlier: 4.525A  pdb=" N   LYS A 431 " --> pdb=" O   VAL A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 469
      removed outlier: 3.923A  pdb=" N   PHE A 467 " --> pdb=" O   LEU A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 490
      Proline residue:  A 482  - end of helix
    Processing helix  chain 'A' and resid 499 through 517
      removed outlier: 3.602A  pdb=" N   LEU A 503 " --> pdb=" O   PRO A 499 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   LEU A 509 " --> pdb=" O   ARG A 505 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   GLN A 510 " --> pdb=" O   CYS A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 534
      removed outlier: 3.560A  pdb=" N   GLY A 523 " --> pdb=" O   LYS A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 560
      removed outlier: 3.755A  pdb=" N   VAL A 546 " --> pdb=" O   MET A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 573
    Processing helix  chain 'A' and resid 577 through 595
    Processing helix  chain 'A' and resid 599 through 614
    Processing helix  chain 'A' and resid 618 through 637
      removed outlier: 4.040A  pdb=" N   TRP A 623 " --> pdb=" O   PRO A 619 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   ALA A 624 " --> pdb=" O   ALA A 620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 663
      removed outlier: 3.678A  pdb=" N   ARG A 654 " --> pdb=" O   LEU A 650 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 669 through 702
    Processing helix  chain 'A' and resid 729 through 737
      removed outlier: 3.988A  pdb=" N   LEU A 737 " --> pdb=" O   ILE A 733 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 759
      removed outlier: 3.700A  pdb=" N   LYS A 745 " --> pdb=" O   ALA A 741 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   CYS A 746 " --> pdb=" O   ALA A 742 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LEU A 747 " --> pdb=" O   GLN A 743 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ALA A 752 " --> pdb=" O   ASP A 748 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 786
    Processing helix  chain 'A' and resid 788 through 806
    Processing helix  chain 'A' and resid 808 through 826
    Processing helix  chain 'A' and resid 829 through 845
      removed outlier: 3.672A  pdb=" N   GLN A 833 " --> pdb=" O   PRO A 829 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   LEU A 834 " --> pdb=" O   SER A 830 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   HIS A 835 " --> pdb=" O   TYR A 831 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   HIS A 845 " --> pdb=" O   SER A 841 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 850 through 871
    Processing helix  chain 'A' and resid 873 through 886
    Processing helix  chain 'A' and resid 887 through 892
      removed outlier: 3.731A  pdb=" N   GLN A 891 " --> pdb=" O   PRO A 888 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LYS A 892 " --> pdb=" O   ALA A 889 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 913
    Processing helix  chain 'A' and resid 920 through 929
    Processing helix  chain 'A' and resid 934 through 954
      removed outlier: 3.610A  pdb=" N   ILE A 950 " --> pdb=" O   LEU A 946 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU A 952 " --> pdb=" O   SER A 948 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 975 through 1001
      removed outlier: 3.742A  pdb=" N   TRP A 981 " --> pdb=" O   LEU A 977 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LEU A 984 " --> pdb=" O   LYS A 980 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   SER A 985 " --> pdb=" O   TRP A 981 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LEU A 998 " --> pdb=" O   LEU A 994 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ARG A1000 " --> pdb=" O   CYS A 996 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1003 through 1022
    Processing helix  chain 'A' and resid 1023 through 1041
      removed outlier: 3.601A  pdb=" N   ARG A1041 " --> pdb=" O   LEU A1037 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1043 through 1062
    Processing helix  chain 'A' and resid 1147 through 1153
    Processing helix  chain 'A' and resid 1153 through 1174
      removed outlier: 3.715A  pdb=" N   ALA A1168 " --> pdb=" O   VAL A1164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1207
      Proline residue:  A1192  - end of helix
    Processing helix  chain 'A' and resid 1217 through 1232
      removed outlier: 4.106A  pdb=" N   GLU A1221 " --> pdb=" O   SER A1217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1232 through 1237
      removed outlier: 4.335A  pdb=" N   ASN A1236 " --> pdb=" O   LEU A1232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1246 through 1257
      removed outlier: 3.767A  pdb=" N   ARG A1257 " --> pdb=" O   PHE A1253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1262 through 1278
      removed outlier: 4.008A  pdb=" N   GLY A1278 " --> pdb=" O   LEU A1274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1573 through 1589
    Processing helix  chain 'A' and resid 1594 through 1608
      removed outlier: 3.794A  pdb=" N   ALA A1598 " --> pdb=" O   SER A1594 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   HIS A1599 " --> pdb=" O   GLY A1595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1612 through 1623
    Processing helix  chain 'A' and resid 1625 through 1647
    Processing helix  chain 'A' and resid 1668 through 1678
    Processing helix  chain 'A' and resid 1688 through 1701
    Processing helix  chain 'A' and resid 1750 through 1768
      removed outlier: 3.617A  pdb=" N   LYS A1765 " --> pdb=" O   GLN A1761 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1772 through 1798
      removed outlier: 3.527A  pdb=" N   GLU A1795 " --> pdb=" O   ILE A1791 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1803 through 1807
      removed outlier: 3.609A  pdb=" N   LEU A1806 " --> pdb=" O   LYS A1803 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1814 through 1830
    Processing helix  chain 'A' and resid 1836 through 1843
    Processing helix  chain 'A' and resid 1845 through 1849
    Processing helix  chain 'A' and resid 1850 through 1862
    Processing helix  chain 'A' and resid 1866 through 1880
    Processing helix  chain 'A' and resid 1903 through 1907
    Processing helix  chain 'A' and resid 1920 through 1934
      removed outlier: 4.099A  pdb=" N   LEU A1924 " --> pdb=" O   SER A1920 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU A1925 " --> pdb=" O   PHE A1921 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   TYR A1933 " --> pdb=" O   ILE A1929 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1936 through 1941
    Processing helix  chain 'A' and resid 1958 through 1972
      removed outlier: 3.865A  pdb=" N   GLN A1964 " --> pdb=" O   SER A1960 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1984 through 1995
      removed outlier: 3.681A  pdb=" N   HIS A1995 " --> pdb=" O   ALA A1991 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2011 through 2017
    Processing helix  chain 'A' and resid 2044 through 2051
      removed outlier: 3.785A  pdb=" N   LYS A2048 " --> pdb=" O   GLY A2044 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2066 through 2084
      removed outlier: 4.711A  pdb=" N   GLY A2082 " --> pdb=" O   GLN A2078 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   GLY A2084 " --> pdb=" O   TRP A2080 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2088 through 2096
      removed outlier: 3.679A  pdb=" N   TYR A2092 " --> pdb=" O   PRO A2088 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ASN A2094 " --> pdb=" O   LEU A2090 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2097 through 2099
      No H-bonds generated for 'chain 'A' and resid 2097 through 2099'
    Processing helix  chain 'B' and resid 121 through 126
      removed outlier: 4.001A  pdb=" N   PHE B 125 " --> pdb=" O   PRO B 122 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1737 through 1742
      removed outlier: 4.458A  pdb=" N   THR A1724 " --> pdb=" O   ALA A1714 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   THR A1707 " --> pdb=" O   VAL A1892 " (cutoff:3.500A)
      removed outlier: 7.260A  pdb=" N   VAL A1894 " --> pdb=" O   THR A1707 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   CYS A1709 " --> pdb=" O   VAL A1894 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1978 through 1979
      removed outlier: 7.771A  pdb=" N   VAL A1978 " --> pdb=" O   THR A1948 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   TYR A1950 " --> pdb=" O   VAL A1978 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   TYR A1998 " --> pdb=" O   LEU A2025 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   PHE A2027 " --> pdb=" O   TYR A1998 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   TYR A2000 " --> pdb=" O   PHE A2027 " (cutoff:3.500A)

    730 hydrogen bonds defined for protein.
    2154 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: 2.03

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2409
        1.33 -     1.46: 2594
        1.46 -     1.58: 6235
        1.58 -     1.71: 0
        1.71 -     1.84: 65
  Bond restraints: 11303
  Sorted by residual:
  bond pdb=" N   VAL A1246 "
       pdb=" CA  VAL A1246 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.039 1.08e-02 8.57e+03 1.31e+01
  bond pdb=" CA  SER A1940 "
       pdb=" CB  SER A1940 "
    ideal  model  delta    sigma   weight residual
    1.535  1.483  0.052 1.69e-02 3.50e+03 9.33e+00
  bond pdb=" N   VAL A1885 "
       pdb=" CA  VAL A1885 "
    ideal  model  delta    sigma   weight residual
    1.461  1.498 -0.037 1.23e-02 6.61e+03 9.04e+00
  bond pdb=" N   LEU A1883 "
       pdb=" CA  LEU A1883 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.034 1.16e-02 7.43e+03 8.83e+00
  bond pdb=" N   GLN B 135 "
       pdb=" CA  GLN B 135 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.23e-02 6.61e+03 8.47e+00
  ... (remaining 11298 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 15065
        2.13 -     4.26: 290
        4.26 -     6.38: 33
        6.38 -     8.51: 7
        8.51 -    10.64: 2
  Bond angle restraints: 15397
  Sorted by residual:
  angle pdb=" N   GLU B 133 "
        pdb=" CA  GLU B 133 "
        pdb=" C   GLU B 133 "
      ideal   model   delta    sigma   weight residual
     113.72  103.08   10.64 1.30e+00 5.92e-01 6.70e+01
  angle pdb=" N   PRO A 331 "
        pdb=" CA  PRO A 331 "
        pdb=" CB  PRO A 331 "
      ideal   model   delta    sigma   weight residual
     103.08  110.20   -7.12 9.70e-01 1.06e+00 5.39e+01
  angle pdb=" N   PRO A 329 "
        pdb=" CA  PRO A 329 "
        pdb=" CB  PRO A 329 "
      ideal   model   delta    sigma   weight residual
     103.25  110.22   -6.97 1.05e+00 9.07e-01 4.41e+01
  angle pdb=" N   PRO A 289 "
        pdb=" CA  PRO A 289 "
        pdb=" CB  PRO A 289 "
      ideal   model   delta    sigma   weight residual
     103.25  110.07   -6.82 1.05e+00 9.07e-01 4.22e+01
  angle pdb=" N   PRO B 131 "
        pdb=" CA  PRO B 131 "
        pdb=" C   PRO B 131 "
      ideal   model   delta    sigma   weight residual
     114.68  121.25   -6.57 1.04e+00 9.25e-01 3.99e+01
  ... (remaining 15392 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 6329
       17.98 -    35.96: 402
       35.96 -    53.94: 82
       53.94 -    71.92: 21
       71.92 -    89.89: 13
  Dihedral angle restraints: 6847
    sinusoidal: 2483
      harmonic: 4364
  Sorted by residual:
  dihedral pdb=" CB  CYS A 637 "
           pdb=" SG  CYS A 637 "
           pdb=" SG  CYS A 687 "
           pdb=" CB  CYS A 687 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -126.47   40.47     1      1.00e+01 1.00e-02 2.30e+01
  dihedral pdb=" C   ILE A1258 "
           pdb=" N   ILE A1258 "
           pdb=" CA  ILE A1258 "
           pdb=" CB  ILE A1258 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -133.16   11.16     0      2.50e+00 1.60e-01 1.99e+01
  dihedral pdb=" CA  VAL B 144 "
           pdb=" C   VAL B 144 "
           pdb=" N   PRO B 145 "
           pdb=" CA  PRO B 145 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.29  -19.71     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 6844 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1607
       0.062 -    0.125: 188
       0.125 -    0.187: 18
       0.187 -    0.249: 5
       0.249 -    0.311: 6
  Chirality restraints: 1824
  Sorted by residual:
  chirality pdb=" CA  PRO B 131 "
            pdb=" N   PRO B 131 "
            pdb=" C   PRO B 131 "
            pdb=" CB  PRO B 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.41    0.31 2.00e-01 2.50e+01 2.42e+00
  chirality pdb=" CA  ILE A1258 "
            pdb=" N   ILE A1258 "
            pdb=" C   ILE A1258 "
            pdb=" CB  ILE A1258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.16    0.28 2.00e-01 2.50e+01 1.93e+00
  chirality pdb=" CA  ARG A1257 "
            pdb=" N   ARG A1257 "
            pdb=" C   ARG A1257 "
            pdb=" CB  ARG A1257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.91e+00
  ... (remaining 1821 not shown)

  Planarity restraints: 1987
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 131 "    0.011 2.00e-02 2.50e+03   2.30e-02 5.31e+00
        pdb=" C   PRO B 131 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   PRO B 131 "    0.015 2.00e-02 2.50e+03
        pdb=" N   GLU B 132 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A1592 "    0.033 5.00e-02 4.00e+02   5.05e-02 4.08e+00
        pdb=" N   PRO A1593 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A1593 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A1593 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A1961 "   -0.010 2.00e-02 2.50e+03   1.96e-02 3.82e+00
        pdb=" C   THR A1961 "    0.034 2.00e-02 2.50e+03
        pdb=" O   THR A1961 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLU A1962 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1984 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1472
        2.75 -     3.29: 11251
        3.29 -     3.82: 18337
        3.82 -     4.36: 21448
        4.36 -     4.90: 36710
  Nonbonded interactions: 89218
  Sorted by model distance:
  nonbonded pdb=" O   PHE A1585 "
            pdb=" OG  SER A1589 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   LYS A 755 "
            pdb=" OG1 THR A 759 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O   PRO A 500 "
            pdb=" ND1 HIS A 504 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" O   GLN A1674 "
            pdb=" OG  SER A1678 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" ND2 ASN A1953 "
            pdb=" OE1 GLU A1962 "
     model   vdw
     2.242 3.120
  ... (remaining 89213 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.910
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.980
  Find NCS groups from input model:        0.060
  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:6.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7000
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  11304  Z= 0.272
  Angle     :  0.698  10.639  15399  Z= 0.433
  Chirality :  0.046   0.311   1824
  Planarity :  0.005   0.050   1987
  Dihedral  : 13.535  89.894   4006
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  7.40 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 10.35 %
    Favored  : 88.56 %
  Cbeta Deviations :  0.07 %
  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: -2.39 (0.19), residues: 1487
  helix: -0.93 (0.14), residues: 985
  sheet: -1.62 (0.66), residues: 48
  loop : -2.85 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1774 
 TYR   0.014   0.001   TYR A1597 
 PHE   0.011   0.001   PHE B 117 
 TRP   0.014   0.002   TRP A 932 
 HIS   0.007   0.001   HIS A1890 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 (11303)
  covalent geometry    : angle       0.69662 (15397)
  SS BOND              : bond        0.00805 (    1)
  SS BOND              : angle       3.41068 (    2)
  hydrogen bonds       : bond        0.13657 (  730)
  hydrogen bonds       : angle       5.60583 ( 2154)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 256
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  462 ASN cc_start: 0.7793 (m110) cc_final: 0.7478 (m-40)
REVERT: A  587 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6607 (mt-10)
REVERT: A  821 GLN cc_start: 0.6980 (tt0) cc_final: 0.6725 (tt0)
REVERT: A  822 LEU cc_start: 0.7909 (tp) cc_final: 0.7645 (tt)
REVERT: A 1054 VAL cc_start: 0.7859 (m) cc_final: 0.7651 (t)
REVERT: A 1946 ARG cc_start: 0.7525 (mtt90) cc_final: 0.7010 (mtp-110)
REVERT: A 2049 TYR cc_start: 0.7846 (m-80) cc_final: 0.7607 (m-80)
REVERT: A 2069 ILE cc_start: 0.8045 (tp) cc_final: 0.7816 (mp)
REVERT: A 2117 VAL cc_start: 0.8471 (m) cc_final: 0.8219 (t)
  outliers start: 12
  outliers final: 5
  residues processed: 266
  average time/residue: 0.5039
  time to fit residues: 145.4157
Evaluate side-chains
  216 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 211
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain A residue  735 PHE
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain B residue  155 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:    0.1980
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    0.0670
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   chunk 122 optimal weight:    0.2980
   chunk 91 optimal weight:    0.6980
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.3518

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

Flipped N/Q/H residues before XYZ refinement:
** A 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 694 GLN
A 866 GLN
A 933 GLN
A1048 GLN
A1176 HIS
A1236 ASN
** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1874 ASN
B 160 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.160328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.134838 restraints weight = 14982.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3810 rms_B_bonded: 1.94
r_work: 0.3693 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3534 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  11304  Z= 0.157
  Angle     :  0.674  12.868  15399  Z= 0.331
  Chirality :  0.039   0.172   1824
  Planarity :  0.005   0.042   1987
  Dihedral  :  5.298  54.336   1597
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.99 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 16.89 %
    Favored  : 79.56 %
  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: -0.76 (0.21), residues: 1487
  helix:  0.39 (0.16), residues: 1006
  sheet: -0.53 (0.71), residues: 46
  loop : -2.59 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1821 
 TYR   0.020   0.001   TYR A 465 
 PHE   0.010   0.001   PHE A1603 
 TRP   0.018   0.001   TRP A2080 
 HIS   0.016   0.001   HIS A1890 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (11303)
  covalent geometry    : angle       0.67299 (15397)
  SS BOND              : bond        0.00639 (    1)
  SS BOND              : angle       2.68355 (    2)
  hydrogen bonds       : bond        0.04517 (  730)
  hydrogen bonds       : angle       4.40645 ( 2154)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 226
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  462 ASN cc_start: 0.8057 (m110) cc_final: 0.7803 (m-40)
REVERT: A  548 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.8034 (t80)
REVERT: A  551 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7354 (ttm170)
REVERT: A  631 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7503 (mp0)
REVERT: A  875 THR cc_start: 0.7951 (OUTLIER) cc_final: 0.7728 (p)
REVERT: A 1054 VAL cc_start: 0.7940 (m) cc_final: 0.7726 (t)
REVERT: A 1151 CYS cc_start: 0.6441 (OUTLIER) cc_final: 0.6144 (t)
REVERT: A 1207 ASN cc_start: 0.8038 (t0) cc_final: 0.7826 (m-40)
REVERT: A 1232 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8211 (tt)
REVERT: A 1252 LYS cc_start: 0.8497 (ttmm) cc_final: 0.8244 (mtpp)
REVERT: A 1756 GLU cc_start: 0.7726 (tp30) cc_final: 0.7367 (tm-30)
REVERT: A 1817 GLN cc_start: 0.6968 (mm-40) cc_final: 0.6680 (mm-40)
REVERT: A 1825 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7485 (mm)
REVERT: A 1946 ARG cc_start: 0.7781 (mtt90) cc_final: 0.7089 (mtt-85)
REVERT: A 2049 TYR cc_start: 0.8269 (m-80) cc_final: 0.7963 (m-80)
REVERT: A 2069 ILE cc_start: 0.8009 (tp) cc_final: 0.7647 (mm)
REVERT: A 2117 VAL cc_start: 0.8755 (m) cc_final: 0.8540 (t)
  outliers start: 39
  outliers final: 11
  residues processed: 244
  average time/residue: 0.5241
  time to fit residues: 138.8479
Evaluate side-chains
  220 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 203
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  544 GLU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  551 ARG
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain A residue  735 PHE
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain A residue  836 LEU
Chi-restraints excluded: chain A residue  875 THR
Chi-restraints excluded: chain A residue  879 SER
Chi-restraints excluded: chain A residue  978 VAL
Chi-restraints excluded: chain A residue 1151 CYS
Chi-restraints excluded: chain A residue 1170 VAL
Chi-restraints excluded: chain A residue 1218 LEU
Chi-restraints excluded: chain A residue 1232 LEU
Chi-restraints excluded: chain A residue 1704 SER
Chi-restraints excluded: chain A residue 1825 LEU
Chi-restraints excluded: chain A residue 1884 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 117 optimal weight:    3.9990
   chunk 118 optimal weight:    0.6980
   chunk 3 optimal weight:    7.9990
   chunk 100 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   chunk 98 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0010
   chunk 25 optimal weight:    4.9990
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 504 HIS
A 565 GLN
A 694 GLN
A 903 GLN
A 997 HIS
** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1874 ASN
B 135 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.158495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.132742 restraints weight = 15102.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3795 rms_B_bonded: 1.94
r_work: 0.3679 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3519 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11304  Z= 0.175
  Angle     :  0.660  10.879  15399  Z= 0.325
  Chirality :  0.041   0.163   1824
  Planarity :  0.005   0.044   1987
  Dihedral  :  4.980  53.051   1593
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.66 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 18.35 %
    Favored  : 77.66 %
  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: -0.17 (0.22), residues: 1487
  helix:  0.87 (0.16), residues: 1009
  sheet: -0.34 (0.71), residues: 48
  loop : -2.47 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1868 
 TYR   0.012   0.001   TYR A 465 
 PHE   0.010   0.001   PHE B 117 
 TRP   0.018   0.002   TRP A 869 
 HIS   0.017   0.001   HIS A1890 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 (11303)
  covalent geometry    : angle       0.65878 (15397)
  SS BOND              : bond        0.00684 (    1)
  SS BOND              : angle       2.93638 (    2)
  hydrogen bonds       : bond        0.04469 (  730)
  hydrogen bonds       : angle       4.22875 ( 2154)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 219
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  631 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7500 (mp0)
REVERT: A  875 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7806 (m)
REVERT: A 1196 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7276 (tm-30)
REVERT: A 1200 GLN cc_start: 0.7665 (mm110) cc_final: 0.7181 (mm110)
REVERT: A 1207 ASN cc_start: 0.8047 (t0) cc_final: 0.7805 (m-40)
REVERT: A 1232 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8239 (tt)
REVERT: A 1252 LYS cc_start: 0.8508 (ttmm) cc_final: 0.8249 (mtpp)
REVERT: A 1756 GLU cc_start: 0.7720 (tp30) cc_final: 0.7312 (tm-30)
REVERT: A 1817 GLN cc_start: 0.7113 (mm-40) cc_final: 0.6830 (mm-40)
REVERT: A 1849 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7877 (tt)
REVERT: A 1874 ASN cc_start: 0.7453 (m-40) cc_final: 0.7135 (m-40)
REVERT: A 1946 ARG cc_start: 0.7730 (mtt90) cc_final: 0.7080 (mtt-85)
REVERT: A 1994 LYS cc_start: 0.7821 (ttpp) cc_final: 0.7550 (ttpp)
REVERT: A 2049 TYR cc_start: 0.8270 (m-80) cc_final: 0.8009 (m-80)
REVERT: A 2068 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6952 (p0)
  outliers start: 44
  outliers final: 13
  residues processed: 242
  average time/residue: 0.5381
  time to fit residues: 140.9712
Evaluate side-chains
  223 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 206
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain A residue  735 PHE
Chi-restraints excluded: chain A residue  875 THR
Chi-restraints excluded: chain A residue  978 VAL
Chi-restraints excluded: chain A residue 1170 VAL
Chi-restraints excluded: chain A residue 1202 LEU
Chi-restraints excluded: chain A residue 1218 LEU
Chi-restraints excluded: chain A residue 1232 LEU
Chi-restraints excluded: chain A residue 1608 LEU
Chi-restraints excluded: chain A residue 1704 SER
Chi-restraints excluded: chain A residue 1825 LEU
Chi-restraints excluded: chain A residue 1849 LEU
Chi-restraints excluded: chain A residue 1968 ASN
Chi-restraints excluded: chain A residue 2068 ASP
Chi-restraints excluded: chain B residue  155 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 101 optimal weight:    0.8980
   chunk 127 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 140 optimal weight:    0.8980
   chunk 133 optimal weight:    1.9990
   chunk 120 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 109 optimal weight:    0.6980
   chunk 74 optimal weight:    0.5980
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 504 HIS
** A 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 694 GLN
** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1865 GLN
** A2037 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2060 ASN
B 135 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.157162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.131221 restraints weight = 15110.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3775 rms_B_bonded: 1.94
r_work: 0.3658 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3498 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  11304  Z= 0.204
  Angle     :  0.682  11.390  15399  Z= 0.334
  Chirality :  0.042   0.167   1824
  Planarity :  0.005   0.059   1987
  Dihedral  :  4.875  54.285   1592
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.92 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 19.98 %
    Favored  : 75.84 %
  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: -0.02 (0.22), residues: 1487
  helix:  0.97 (0.16), residues: 1013
  sheet: -0.40 (0.72), residues: 48
  loop : -2.39 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 586 
 TYR   0.016   0.002   TYR A 911 
 PHE   0.015   0.002   PHE B 128 
 TRP   0.021   0.002   TRP A 932 
 HIS   0.016   0.001   HIS A1890 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 (11303)
  covalent geometry    : angle       0.68074 (15397)
  SS BOND              : bond        0.00825 (    1)
  SS BOND              : angle       3.40833 (    2)
  hydrogen bonds       : bond        0.04556 (  730)
  hydrogen bonds       : angle       4.21283 ( 2154)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 213
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  455 MET cc_start: 0.6681 (ptp) cc_final: 0.6184 (ptp)
REVERT: A  631 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7240 (mm-30)
REVERT: A  875 THR cc_start: 0.8015 (OUTLIER) cc_final: 0.7788 (m)
REVERT: A 1200 GLN cc_start: 0.7644 (mm110) cc_final: 0.7427 (mm-40)
REVERT: A 1207 ASN cc_start: 0.8040 (t0) cc_final: 0.7829 (m-40)
REVERT: A 1252 LYS cc_start: 0.8528 (ttmm) cc_final: 0.8277 (mtpp)
REVERT: A 1756 GLU cc_start: 0.7760 (tp30) cc_final: 0.7330 (tm-30)
REVERT: A 1817 GLN cc_start: 0.7135 (mm-40) cc_final: 0.6853 (mm-40)
REVERT: A 1825 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7632 (mm)
REVERT: A 1840 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.7075 (tttm)
REVERT: A 1946 ARG cc_start: 0.7647 (mtt90) cc_final: 0.7049 (mtt-85)
REVERT: A 1986 GLU cc_start: 0.6547 (tm-30) cc_final: 0.6255 (tm-30)
REVERT: A 1990 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7406 (pt0)
REVERT: A 1994 LYS cc_start: 0.7842 (ttpp) cc_final: 0.7610 (ttpp)
REVERT: A 2010 LEU cc_start: 0.8046 (tp) cc_final: 0.7752 (tp)
REVERT: A 2049 TYR cc_start: 0.8323 (m-80) cc_final: 0.7996 (m-80)
REVERT: A 2101 ARG cc_start: 0.7853 (mtt-85) cc_final: 0.7645 (mtt-85)
  outliers start: 46
  outliers final: 18
  residues processed: 237
  average time/residue: 0.5550
  time to fit residues: 142.2596
Evaluate side-chains
  225 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 203
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  544 GLU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain A residue  735 PHE
Chi-restraints excluded: chain A residue  836 LEU
Chi-restraints excluded: chain A residue  875 THR
Chi-restraints excluded: chain A residue  978 VAL
Chi-restraints excluded: chain A residue 1054 VAL
Chi-restraints excluded: chain A residue 1176 HIS
Chi-restraints excluded: chain A residue 1199 THR
Chi-restraints excluded: chain A residue 1202 LEU
Chi-restraints excluded: chain A residue 1218 LEU
Chi-restraints excluded: chain A residue 1232 LEU
Chi-restraints excluded: chain A residue 1704 SER
Chi-restraints excluded: chain A residue 1825 LEU
Chi-restraints excluded: chain A residue 1840 LYS
Chi-restraints excluded: chain A residue 1899 LEU
Chi-restraints excluded: chain A residue 1990 GLU
Chi-restraints excluded: chain A residue 2117 VAL
Chi-restraints excluded: chain B residue  155 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 126 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 56 optimal weight:    0.3980
   chunk 142 optimal weight:    1.9990
   chunk 89 optimal weight:    0.6980
   chunk 136 optimal weight:    0.8980
   chunk 129 optimal weight:    0.5980
   chunk 130 optimal weight:    0.4980
   chunk 36 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0030
   overall best weight:    0.4390

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

Flipped N/Q/H residues before XYZ refinement:
A 504 HIS
A 565 GLN
** A 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 872 GLN
** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2037 HIS
B 135 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.158572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.132761 restraints weight = 14878.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3796 rms_B_bonded: 1.92
r_work: 0.3680 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3522 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.2641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  11304  Z= 0.150
  Angle     :  0.637  11.251  15399  Z= 0.311
  Chirality :  0.040   0.159   1824
  Planarity :  0.005   0.054   1987
  Dihedral  :  4.760  52.549   1592
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.25 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 21.07 %
    Favored  : 74.84 %
  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:  0.36 (0.22), residues: 1487
  helix:  1.29 (0.17), residues: 1011
  sheet: -0.37 (0.73), residues: 48
  loop : -2.32 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 586 
 TYR   0.012   0.001   TYR A 911 
 PHE   0.013   0.001   PHE B 128 
 TRP   0.024   0.002   TRP A 981 
 HIS   0.010   0.001   HIS A1890 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (11303)
  covalent geometry    : angle       0.63598 (15397)
  SS BOND              : bond        0.00547 (    1)
  SS BOND              : angle       2.84740 (    2)
  hydrogen bonds       : bond        0.04062 (  730)
  hydrogen bonds       : angle       4.06876 ( 2154)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 210
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  455 MET cc_start: 0.6594 (ptp) cc_final: 0.6017 (ptp)
REVERT: A  631 GLU cc_start: 0.7515 (mm-30) cc_final: 0.6999 (mm-30)
REVERT: A  876 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8156 (mttt)
REVERT: A  982 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7339 (mm-40)
REVERT: A 1200 GLN cc_start: 0.7683 (mm110) cc_final: 0.7447 (mm-40)
REVERT: A 1207 ASN cc_start: 0.8013 (t0) cc_final: 0.7805 (m-40)
REVERT: A 1232 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8164 (tt)
REVERT: A 1252 LYS cc_start: 0.8521 (ttmm) cc_final: 0.8270 (mtpp)
REVERT: A 1751 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7402 (mtp180)
REVERT: A 1756 GLU cc_start: 0.7807 (tp30) cc_final: 0.7356 (tm-30)
REVERT: A 1825 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7623 (mm)
REVERT: A 1840 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.7063 (tttm)
REVERT: A 1946 ARG cc_start: 0.7629 (mtt90) cc_final: 0.7053 (mtt-85)
REVERT: A 1994 LYS cc_start: 0.7783 (ttpp) cc_final: 0.7448 (ttpp)
REVERT: A 2049 TYR cc_start: 0.8244 (m-80) cc_final: 0.7988 (m-80)
REVERT: A 2101 ARG cc_start: 0.7834 (mtt-85) cc_final: 0.7609 (mtt-85)
  outliers start: 45
  outliers final: 16
  residues processed: 236
  average time/residue: 0.5418
  time to fit residues: 138.3482
Evaluate side-chains
  218 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 196
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  544 GLU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain A residue  735 PHE
Chi-restraints excluded: chain A residue  836 LEU
Chi-restraints excluded: chain A residue  876 LYS
Chi-restraints excluded: chain A residue  971 LEU
Chi-restraints excluded: chain A residue  978 VAL
Chi-restraints excluded: chain A residue  982 GLN
Chi-restraints excluded: chain A residue 1202 LEU
Chi-restraints excluded: chain A residue 1218 LEU
Chi-restraints excluded: chain A residue 1232 LEU
Chi-restraints excluded: chain A residue 1704 SER
Chi-restraints excluded: chain A residue 1751 ARG
Chi-restraints excluded: chain A residue 1810 SER
Chi-restraints excluded: chain A residue 1825 LEU
Chi-restraints excluded: chain A residue 1840 LYS
Chi-restraints excluded: chain A residue 1899 LEU
Chi-restraints excluded: chain B residue  121 ASN
Chi-restraints excluded: chain B residue  155 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 68 optimal weight:    0.1980
   chunk 138 optimal weight:    0.9990
   chunk 49 optimal weight:    0.3980
   chunk 100 optimal weight:    0.9980
   chunk 142 optimal weight:    0.9980
   chunk 110 optimal weight:    0.3980
   chunk 126 optimal weight:    0.2980
   chunk 25 optimal weight:    0.6980
   chunk 144 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 8 optimal weight:    0.2980
   overall best weight:    0.3180

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

Flipped N/Q/H residues before XYZ refinement:
A 504 HIS
** A 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1225 GLN
** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2037 HIS
B 135 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.159915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.133213 restraints weight = 15084.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3799 rms_B_bonded: 2.07
r_work: 0.3676 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3514 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
moved from start:          0.2811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  11304  Z= 0.137
  Angle     :  0.632  10.527  15399  Z= 0.307
  Chirality :  0.039   0.238   1824
  Planarity :  0.004   0.046   1987
  Dihedral  :  4.673  50.852   1592
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.12 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 22.52 %
    Favored  : 74.39 %
  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:  0.62 (0.23), residues: 1487
  helix:  1.49 (0.17), residues: 1011
  sheet: -0.35 (0.74), residues: 48
  loop : -2.22 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 586 
 TYR   0.017   0.001   TYR A2104 
 PHE   0.013   0.001   PHE B 128 
 TRP   0.025   0.002   TRP A 869 
 HIS   0.009   0.001   HIS A1890 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (11303)
  covalent geometry    : angle       0.63176 (15397)
  SS BOND              : bond        0.00651 (    1)
  SS BOND              : angle       2.67253 (    2)
  hydrogen bonds       : bond        0.03881 (  730)
  hydrogen bonds       : angle       3.99647 ( 2154)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 207
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  455 MET cc_start: 0.6685 (ptp) cc_final: 0.6434 (ptp)
REVERT: A  631 GLU cc_start: 0.7533 (mm-30) cc_final: 0.6977 (mm-30)
REVERT: A  876 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8133 (mttt)
REVERT: A  982 GLN cc_start: 0.7643 (mm110) cc_final: 0.7357 (mm-40)
REVERT: A 1200 GLN cc_start: 0.7709 (mm110) cc_final: 0.7246 (mm110)
REVERT: A 1207 ASN cc_start: 0.7984 (t0) cc_final: 0.7783 (m-40)
REVERT: A 1232 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8155 (tt)
REVERT: A 1252 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8258 (mtpp)
REVERT: A 1751 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7370 (mtp180)
REVERT: A 1756 GLU cc_start: 0.7860 (tp30) cc_final: 0.7404 (tm-30)
REVERT: A 1825 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7548 (mm)
REVERT: A 1840 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7148 (tttm)
REVERT: A 1946 ARG cc_start: 0.7556 (mtt90) cc_final: 0.6962 (mtt-85)
REVERT: A 1994 LYS cc_start: 0.7836 (ttpp) cc_final: 0.7601 (ttpp)
REVERT: A 2101 ARG cc_start: 0.7963 (mtt-85) cc_final: 0.7659 (mpt-90)
  outliers start: 34
  outliers final: 12
  residues processed: 224
  average time/residue: 0.5528
  time to fit residues: 133.9947
Evaluate side-chains
  220 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 203
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain A residue  735 PHE
Chi-restraints excluded: chain A residue  836 LEU
Chi-restraints excluded: chain A residue  876 LYS
Chi-restraints excluded: chain A residue  978 VAL
Chi-restraints excluded: chain A residue 1189 LYS
Chi-restraints excluded: chain A residue 1202 LEU
Chi-restraints excluded: chain A residue 1232 LEU
Chi-restraints excluded: chain A residue 1704 SER
Chi-restraints excluded: chain A residue 1751 ARG
Chi-restraints excluded: chain A residue 1825 LEU
Chi-restraints excluded: chain A residue 1840 LYS
Chi-restraints excluded: chain A residue 1899 LEU
Chi-restraints excluded: chain B residue  121 ASN
Chi-restraints excluded: chain B residue  155 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 96 optimal weight:    0.4980
   chunk 137 optimal weight:    0.9990
   chunk 36 optimal weight:    0.2980
   chunk 59 optimal weight:    0.8980
   chunk 72 optimal weight:    0.7980
   chunk 118 optimal weight:    0.8980
   chunk 76 optimal weight:    0.5980
   chunk 92 optimal weight:    0.6980
   chunk 146 optimal weight:    0.0980
   chunk 51 optimal weight:    0.6980
   chunk 109 optimal weight:    0.7980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 504 HIS
** A 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1225 GLN
** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2037 HIS
B 135 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.158827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.132936 restraints weight = 14932.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3799 rms_B_bonded: 1.94
r_work: 0.3683 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3526 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.2952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  11304  Z= 0.150
  Angle     :  0.648  10.711  15399  Z= 0.314
  Chirality :  0.040   0.171   1824
  Planarity :  0.004   0.047   1987
  Dihedral  :  4.665  51.375   1592
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.32 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 23.16 %
    Favored  : 73.66 %
  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:  0.70 (0.22), residues: 1487
  helix:  1.55 (0.16), residues: 1012
  sheet: -0.35 (0.74), residues: 48
  loop : -2.18 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A1868 
 TYR   0.012   0.001   TYR A 911 
 PHE   0.019   0.001   PHE A1603 
 TRP   0.029   0.002   TRP A 869 
 HIS   0.008   0.001   HIS A1890 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (11303)
  covalent geometry    : angle       0.64771 (15397)
  SS BOND              : bond        0.00764 (    1)
  SS BOND              : angle       2.80150 (    2)
  hydrogen bonds       : bond        0.03964 (  730)
  hydrogen bonds       : angle       4.00855 ( 2154)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 208
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  526 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8227 (tpp)
REVERT: A  612 GLU cc_start: 0.7732 (tt0) cc_final: 0.7519 (tt0)
REVERT: A  631 GLU cc_start: 0.7488 (mm-30) cc_final: 0.6943 (mm-30)
REVERT: A  876 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8153 (mttt)
REVERT: A  894 SER cc_start: 0.7880 (t) cc_final: 0.7619 (m)
REVERT: A  982 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7347 (mm-40)
REVERT: A 1200 GLN cc_start: 0.7671 (mm110) cc_final: 0.7255 (mm110)
REVERT: A 1252 LYS cc_start: 0.8514 (ttmm) cc_final: 0.8261 (mtpp)
REVERT: A 1756 GLU cc_start: 0.7764 (tp30) cc_final: 0.7366 (tm-30)
REVERT: A 1825 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7554 (mm)
REVERT: A 1840 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7143 (tttm)
REVERT: A 1874 ASN cc_start: 0.7403 (m-40) cc_final: 0.7133 (m-40)
REVERT: A 1946 ARG cc_start: 0.7660 (mtt90) cc_final: 0.7023 (mtt-85)
REVERT: A 1994 LYS cc_start: 0.7719 (ttpp) cc_final: 0.7471 (ttpp)
REVERT: A 2010 LEU cc_start: 0.7976 (tp) cc_final: 0.7692 (tp)
REVERT: A 2101 ARG cc_start: 0.7790 (mtt-85) cc_final: 0.7514 (mpt-90)
REVERT: A 2104 TYR cc_start: 0.6414 (m-80) cc_final: 0.6188 (m-80)
REVERT: B  121 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7541 (m-40)
  outliers start: 35
  outliers final: 16
  residues processed: 228
  average time/residue: 0.5618
  time to fit residues: 138.5440
Evaluate side-chains
  226 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 204
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  544 GLU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain A residue  735 PHE
Chi-restraints excluded: chain A residue  876 LYS
Chi-restraints excluded: chain A residue  887 ASP
Chi-restraints excluded: chain A residue  971 LEU
Chi-restraints excluded: chain A residue  978 VAL
Chi-restraints excluded: chain A residue  982 GLN
Chi-restraints excluded: chain A residue 1176 HIS
Chi-restraints excluded: chain A residue 1189 LYS
Chi-restraints excluded: chain A residue 1202 LEU
Chi-restraints excluded: chain A residue 1232 LEU
Chi-restraints excluded: chain A residue 1704 SER
Chi-restraints excluded: chain A residue 1825 LEU
Chi-restraints excluded: chain A residue 1840 LYS
Chi-restraints excluded: chain A residue 1899 LEU
Chi-restraints excluded: chain B residue  121 ASN
Chi-restraints excluded: chain B residue  155 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 92 optimal weight:    0.5980
   chunk 107 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 111 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   chunk 42 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 99 optimal weight:    0.7980
   chunk 67 optimal weight:    0.5980
   chunk 122 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 504 HIS
** A 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1048 GLN
A1225 GLN
** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2037 HIS
A2060 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.157353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.131320 restraints weight = 14989.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 1.93
r_work: 0.3663 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3502 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  11304  Z= 0.191
  Angle     :  0.700  12.890  15399  Z= 0.339
  Chirality :  0.042   0.224   1824
  Planarity :  0.005   0.056   1987
  Dihedral  :  4.749  53.288   1592
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.52 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 23.61 %
    Favored  : 73.21 %
  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:  0.56 (0.22), residues: 1487
  helix:  1.41 (0.16), residues: 1019
  sheet: -0.44 (0.72), residues: 48
  loop : -2.20 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A1868 
 TYR   0.022   0.002   TYR A 473 
 PHE   0.017   0.002   PHE A1603 
 TRP   0.032   0.002   TRP A2080 
 HIS   0.009   0.001   HIS A1890 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 (11303)
  covalent geometry    : angle       0.69957 (15397)
  SS BOND              : bond        0.00889 (    1)
  SS BOND              : angle       3.18076 (    2)
  hydrogen bonds       : bond        0.04315 (  730)
  hydrogen bonds       : angle       4.12237 ( 2154)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 206
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  526 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8144 (tpp)
REVERT: A  631 GLU cc_start: 0.7429 (mm-30) cc_final: 0.6882 (mm-30)
REVERT: A  876 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8141 (mttt)
REVERT: A  894 SER cc_start: 0.7905 (t) cc_final: 0.7655 (m)
REVERT: A  982 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7357 (mm-40)
REVERT: A 1200 GLN cc_start: 0.7681 (mm110) cc_final: 0.7325 (mm110)
REVERT: A 1252 LYS cc_start: 0.8531 (ttmm) cc_final: 0.8298 (mtpp)
REVERT: A 1751 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7936 (ttp-170)
REVERT: A 1756 GLU cc_start: 0.7801 (tp30) cc_final: 0.7391 (tm-30)
REVERT: A 1825 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7574 (mm)
REVERT: A 1840 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7121 (tttm)
REVERT: A 1946 ARG cc_start: 0.7641 (mtt90) cc_final: 0.7029 (mtt-85)
REVERT: A 1994 LYS cc_start: 0.7788 (ttpp) cc_final: 0.7580 (ttpp)
REVERT: A 2010 LEU cc_start: 0.8000 (tp) cc_final: 0.7791 (tp)
REVERT: A 2101 ARG cc_start: 0.7840 (mtt-85) cc_final: 0.7559 (mpt-90)
  outliers start: 35
  outliers final: 19
  residues processed: 225
  average time/residue: 0.5505
  time to fit residues: 134.1459
Evaluate side-chains
  223 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 198
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  544 GLU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain A residue  735 PHE
Chi-restraints excluded: chain A residue  836 LEU
Chi-restraints excluded: chain A residue  876 LYS
Chi-restraints excluded: chain A residue  887 ASP
Chi-restraints excluded: chain A residue  971 LEU
Chi-restraints excluded: chain A residue  978 VAL
Chi-restraints excluded: chain A residue  982 GLN
Chi-restraints excluded: chain A residue 1176 HIS
Chi-restraints excluded: chain A residue 1186 VAL
Chi-restraints excluded: chain A residue 1189 LYS
Chi-restraints excluded: chain A residue 1199 THR
Chi-restraints excluded: chain A residue 1202 LEU
Chi-restraints excluded: chain A residue 1232 LEU
Chi-restraints excluded: chain A residue 1704 SER
Chi-restraints excluded: chain A residue 1751 ARG
Chi-restraints excluded: chain A residue 1825 LEU
Chi-restraints excluded: chain A residue 1840 LYS
Chi-restraints excluded: chain A residue 1899 LEU
Chi-restraints excluded: chain B residue  155 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0000
   chunk 91 optimal weight:    0.7980
   chunk 115 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 118 optimal weight:    0.8980
   chunk 146 optimal weight:    0.0870
   chunk 59 optimal weight:    0.6980
   chunk 145 optimal weight:    0.0170
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.3200

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

Flipped N/Q/H residues before XYZ refinement:
A 504 HIS
** A 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1225 GLN
** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1874 ASN
A2037 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.160092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.133960 restraints weight = 14854.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3807 rms_B_bonded: 1.93
r_work: 0.3691 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3531 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.3177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  11304  Z= 0.140
  Angle     :  0.672  12.790  15399  Z= 0.323
  Chirality :  0.040   0.161   1824
  Planarity :  0.005   0.061   1987
  Dihedral  :  4.670  51.104   1592
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.19 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 24.89 %
    Favored  : 72.30 %
  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:  0.81 (0.23), residues: 1487
  helix:  1.62 (0.17), residues: 1018
  sheet: -0.38 (0.73), residues: 48
  loop : -2.15 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A1868 
 TYR   0.011   0.001   TYR A1933 
 PHE   0.014   0.001   PHE A1603 
 TRP   0.034   0.002   TRP A 869 
 HIS   0.007   0.001   HIS A1176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (11303)
  covalent geometry    : angle       0.67138 (15397)
  SS BOND              : bond        0.00613 (    1)
  SS BOND              : angle       2.66015 (    2)
  hydrogen bonds       : bond        0.03882 (  730)
  hydrogen bonds       : angle       4.05591 ( 2154)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 203
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  526 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8266 (tpp)
REVERT: A  587 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7360 (tt0)
REVERT: A  631 GLU cc_start: 0.7496 (mm-30) cc_final: 0.6948 (mm-30)
REVERT: A  894 SER cc_start: 0.7862 (t) cc_final: 0.7610 (m)
REVERT: A  982 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7326 (mm-40)
REVERT: A 1200 GLN cc_start: 0.7662 (mm110) cc_final: 0.7303 (mm110)
REVERT: A 1232 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8049 (tt)
REVERT: A 1252 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8258 (mtpp)
REVERT: A 1751 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7383 (mtp180)
REVERT: A 1756 GLU cc_start: 0.7803 (tp30) cc_final: 0.7392 (tm-30)
REVERT: A 1807 LEU cc_start: 0.8782 (mm) cc_final: 0.8500 (mp)
REVERT: A 1825 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7573 (mm)
REVERT: A 1840 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7210 (tttm)
REVERT: A 1874 ASN cc_start: 0.7407 (m-40) cc_final: 0.7142 (m-40)
REVERT: A 1946 ARG cc_start: 0.7623 (mtt90) cc_final: 0.7017 (mtt-85)
REVERT: A 2101 ARG cc_start: 0.7860 (mtt-85) cc_final: 0.7572 (mpt-90)
  outliers start: 31
  outliers final: 18
  residues processed: 221
  average time/residue: 0.5413
  time to fit residues: 129.6770
Evaluate side-chains
  219 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 194
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  587 GLU
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain A residue  735 PHE
Chi-restraints excluded: chain A residue  836 LEU
Chi-restraints excluded: chain A residue  887 ASP
Chi-restraints excluded: chain A residue  971 LEU
Chi-restraints excluded: chain A residue  978 VAL
Chi-restraints excluded: chain A residue  982 GLN
Chi-restraints excluded: chain A residue 1060 SER
Chi-restraints excluded: chain A residue 1176 HIS
Chi-restraints excluded: chain A residue 1186 VAL
Chi-restraints excluded: chain A residue 1189 LYS
Chi-restraints excluded: chain A residue 1202 LEU
Chi-restraints excluded: chain A residue 1232 LEU
Chi-restraints excluded: chain A residue 1704 SER
Chi-restraints excluded: chain A residue 1751 ARG
Chi-restraints excluded: chain A residue 1793 SER
Chi-restraints excluded: chain A residue 1825 LEU
Chi-restraints excluded: chain A residue 1840 LYS
Chi-restraints excluded: chain A residue 1899 LEU
Chi-restraints excluded: chain B residue  155 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 105 optimal weight:    0.9980
   chunk 137 optimal weight:    0.7980
   chunk 81 optimal weight:    0.8980
   chunk 66 optimal weight:    0.2980
   chunk 134 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 116 optimal weight:    0.8980
   chunk 127 optimal weight:    0.5980
   chunk 124 optimal weight:    0.0870
   chunk 90 optimal weight:    0.6980
   chunk 120 optimal weight:    0.6980
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
** A 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1225 GLN
** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2037 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.158587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.132418 restraints weight = 14871.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.3797 rms_B_bonded: 1.94
r_work: 0.3680 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3520 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.3266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  11304  Z= 0.160
  Angle     :  0.696  13.976  15399  Z= 0.335
  Chirality :  0.041   0.227   1824
  Planarity :  0.005   0.064   1987
  Dihedral  :  4.682  51.955   1592
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.32 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 25.70 %
    Favored  : 71.93 %
  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:  0.78 (0.23), residues: 1487
  helix:  1.58 (0.16), residues: 1024
  sheet: -0.37 (0.72), residues: 48
  loop : -2.17 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A1868 
 TYR   0.013   0.001   TYR A 911 
 PHE   0.016   0.001   PHE A1603 
 TRP   0.040   0.002   TRP A2080 
 HIS   0.008   0.001   HIS A1176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (11303)
  covalent geometry    : angle       0.69515 (15397)
  SS BOND              : bond        0.00764 (    1)
  SS BOND              : angle       2.92889 (    2)
  hydrogen bonds       : bond        0.04032 (  730)
  hydrogen bonds       : angle       4.07719 ( 2154)

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

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

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2974 Ramachandran restraints generated.
    1487 Oldfield, 0 Emsley, 1487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 198
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  513 SER cc_start: 0.8052 (t) cc_final: 0.7715 (p)
REVERT: A  526 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8321 (tpp)
REVERT: A  631 GLU cc_start: 0.7442 (mm-30) cc_final: 0.6884 (mm-30)
REVERT: A  644 GLN cc_start: 0.6907 (mp10) cc_final: 0.6623 (mp10)
REVERT: A  894 SER cc_start: 0.7896 (t) cc_final: 0.7653 (m)
REVERT: A  982 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7335 (mm-40)
REVERT: A 1200 GLN cc_start: 0.7677 (mm110) cc_final: 0.7314 (mm110)
REVERT: A 1252 LYS cc_start: 0.8517 (ttmm) cc_final: 0.8273 (mtpp)
REVERT: A 1751 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7362 (mtp180)
REVERT: A 1756 GLU cc_start: 0.7793 (tp30) cc_final: 0.7388 (tm-30)
REVERT: A 1807 LEU cc_start: 0.8757 (mm) cc_final: 0.8481 (mp)
REVERT: A 1825 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7608 (mm)
REVERT: A 1840 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.7092 (tttm)
REVERT: A 1946 ARG cc_start: 0.7623 (mtt90) cc_final: 0.7009 (mtt-85)
REVERT: A 1994 LYS cc_start: 0.7810 (ttpp) cc_final: 0.7494 (ttpp)
REVERT: A 2101 ARG cc_start: 0.7863 (mtt-85) cc_final: 0.7572 (mpt-90)
  outliers start: 26
  outliers final: 18
  residues processed: 215
  average time/residue: 0.5165
  time to fit residues: 120.5960
Evaluate side-chains
  220 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 197
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  687 CYS
Chi-restraints excluded: chain A residue  735 PHE
Chi-restraints excluded: chain A residue  887 ASP
Chi-restraints excluded: chain A residue  971 LEU
Chi-restraints excluded: chain A residue  978 VAL
Chi-restraints excluded: chain A residue  982 GLN
Chi-restraints excluded: chain A residue 1060 SER
Chi-restraints excluded: chain A residue 1176 HIS
Chi-restraints excluded: chain A residue 1186 VAL
Chi-restraints excluded: chain A residue 1189 LYS
Chi-restraints excluded: chain A residue 1202 LEU
Chi-restraints excluded: chain A residue 1232 LEU
Chi-restraints excluded: chain A residue 1704 SER
Chi-restraints excluded: chain A residue 1751 ARG
Chi-restraints excluded: chain A residue 1793 SER
Chi-restraints excluded: chain A residue 1825 LEU
Chi-restraints excluded: chain A residue 1840 LYS
Chi-restraints excluded: chain A residue 1899 LEU
Chi-restraints excluded: chain B residue  155 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 149
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 105 optimal weight:    0.7980
   chunk 92 optimal weight:    0.5980
   chunk 43 optimal weight:    0.3980
   chunk 23 optimal weight:    0.4980
   chunk 79 optimal weight:    0.9990
   chunk 140 optimal weight:    0.7980
   chunk 50 optimal weight:    0.6980
   chunk 135 optimal weight:    0.6980
   chunk 130 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** A 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1053 GLN
A1225 GLN
** A1637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2037 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.159634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.133178 restraints weight = 14847.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3793 rms_B_bonded: 1.94
r_work: 0.3675 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3512 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.3318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  11304  Z= 0.157
  Angle     :  0.692  14.231  15399  Z= 0.334
  Chirality :  0.041   0.228   1824
  Planarity :  0.005   0.048   1987
  Dihedral  :  4.661  51.563   1592
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.19 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 25.43 %
    Favored  : 72.21 %
  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:  0.81 (0.23), residues: 1487
  helix:  1.61 (0.16), residues: 1023
  sheet: -0.31 (0.72), residues: 48
  loop : -2.15 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A2021 
 TYR   0.015   0.001   TYR A1933 
 PHE   0.015   0.001   PHE A1603 
 TRP   0.045   0.003   TRP A2080 
 HIS   0.008   0.001   HIS A1176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (11303)
  covalent geometry    : angle       0.69151 (15397)
  SS BOND              : bond        0.00722 (    1)
  SS BOND              : angle       2.82889 (    2)
  hydrogen bonds       : bond        0.03983 (  730)
  hydrogen bonds       : angle       4.06641 ( 2154)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4413.07 seconds
wall clock time: 75 minutes 50.00 seconds (4550.00 seconds total)