Starting phenix.real_space_refine
on Wed Feb 12 07:08:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6oeu_7795/02_2025/6oeu_7795.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6oeu_7795/02_2025/6oeu_7795.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6oeu_7795/02_2025/6oeu_7795.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6oeu_7795/02_2025/6oeu_7795.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6oeu_7795/02_2025/6oeu_7795.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6oeu_7795/02_2025/6oeu_7795.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.103
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      34      5.16       5
     C    4734      2.51       5
     N    1215      2.21       5
     O    1327      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7310
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7198
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 964, 7198
          Classifications: {'peptide': 964}
          Incomplete info: {'truncation_to_alanine': 116}
          Link IDs: {'PTRANS': 39, 'TRANS': 924}
          Chain breaks: 2
          Unresolved chain link angles: 7
          Unresolved non-hydrogen bonds: 464
          Unresolved non-hydrogen angles: 603
          Unresolved non-hydrogen dihedrals: 406
          Unresolved non-hydrogen chiralities: 33
          Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 11, 'ASN:plan1': 8, 'TRP:plan': 5, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 267
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 5.05, per 1000 atoms: 0.69
  Number of scatterers: 7310
  At special positions: 0
  Unit cell: (133, 83, 87, 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      34     16.00
     O    1327      8.00
     N    1215      7.00
     C    4734      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG E   1 " - " ASN A1000 "
  Time building additional restraints: 1.79
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1808

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 4 sheets defined
      59.0% alpha, 2.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 77 through 94
      removed outlier: 4.616A  pdb=" N   LEU A  87 " --> pdb=" O   PHE A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 116
      removed outlier: 3.692A  pdb=" N   GLY A 105 " --> pdb=" O   PHE A 101 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   PHE A 112 " --> pdb=" O   ILE A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 146
      removed outlier: 4.015A  pdb=" N   ARG A 138 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 187
    Processing helix  chain 'A' and resid 215 through 222
    Processing helix  chain 'A' and resid 230 through 235
      removed outlier: 3.991A  pdb=" N   CYS A 234 " --> pdb=" O   PRO A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 271
      removed outlier: 3.676A  pdb=" N   ILE A 271 " --> pdb=" O   GLU A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 283
    Processing helix  chain 'A' and resid 338 through 342
      removed outlier: 3.834A  pdb=" N   ILE A 342 " --> pdb=" O   GLN A 338 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 338 through 342'
    Processing helix  chain 'A' and resid 368 through 376
    Processing helix  chain 'A' and resid 388 through 409
      removed outlier: 3.606A  pdb=" N   GLN A 409 " --> pdb=" O   GLU A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 436
    Processing helix  chain 'A' and resid 438 through 456
      removed outlier: 3.603A  pdb=" N   VAL A 442 " --> pdb=" O   SER A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 491
    Processing helix  chain 'A' and resid 502 through 525
      removed outlier: 4.478A  pdb=" N   LEU A 508 " --> pdb=" O   PRO A 504 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LEU A 517 " --> pdb=" O   ASP A 513 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   LEU A 518 " --> pdb=" O   ASP A 514 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   THR A 525 " --> pdb=" O   ALA A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 561
      removed outlier: 5.271A  pdb=" N   ALA A 546 " --> pdb=" O   LYS A 542 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   SER A 547 " --> pdb=" O   ARG A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 602
      Proline residue:  A 593  - end of helix
      removed outlier: 3.559A  pdb=" N   ARG A 602 " --> pdb=" O   MET A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 732 through 741
    Processing helix  chain 'A' and resid 746 through 770
    Processing helix  chain 'A' and resid 776 through 780
      removed outlier: 3.660A  pdb=" N   ASP A 779 " --> pdb=" O   ASP A 776 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 798
      removed outlier: 3.843A  pdb=" N   ASP A 789 " --> pdb=" O   THR A 785 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 816 through 825
    Processing helix  chain 'A' and resid 834 through 838
      removed outlier: 3.980A  pdb=" N   ASN A 837 " --> pdb=" O   LEU A 834 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   LYS A 838 " --> pdb=" O   GLU A 835 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 834 through 838'
    Processing helix  chain 'A' and resid 843 through 866
      removed outlier: 3.627A  pdb=" N   TYR A 847 " --> pdb=" O   MET A 843 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR A 865 " --> pdb=" O   SER A 861 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 877 through 887
    Processing helix  chain 'A' and resid 918 through 930
      removed outlier: 3.674A  pdb=" N   SER A 928 " --> pdb=" O   THR A 924 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 930 through 938
      removed outlier: 3.595A  pdb=" N   TYR A 934 " --> pdb=" O   ASP A 930 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 985 through 1004
      removed outlier: 3.689A  pdb=" N   LEU A1004 " --> pdb=" O   ASN A1000 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1018
      removed outlier: 3.549A  pdb=" N   TRP A1018 " --> pdb=" O   PRO A1014 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1023 through 1048
      removed outlier: 3.537A  pdb=" N   TRP A1027 " --> pdb=" O   GLY A1023 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1049 through 1075
    Processing helix  chain 'A' and resid 1079 through 1102
      removed outlier: 4.105A  pdb=" N   VAL A1090 " --> pdb=" O   LEU A1086 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   GLY A1091 " --> pdb=" O   ILE A1087 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   GLU A1095 " --> pdb=" O   GLY A1091 " (cutoff:3.500A)
      removed outlier: 4.763A  pdb=" N   PHE A1096 " --> pdb=" O   ILE A1092 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1103 through 1106
      removed outlier: 3.685A  pdb=" N   THR A1106 " --> pdb=" O   ALA A1103 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1103 through 1106'
    Processing helix  chain 'A' and resid 1112 through 1138
      removed outlier: 3.574A  pdb=" N   VAL A1116 " --> pdb=" O   ASN A1112 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   MET A1122 " --> pdb=" O   ALA A1118 " (cutoff:3.500A)
      removed outlier: 5.199A  pdb=" N   ALA A1124 " --> pdb=" O   GLU A1120 " (cutoff:3.500A)
      Proline residue:  A1125  - end of helix
    Processing helix  chain 'A' and resid 1139 through 1142
    Processing helix  chain 'A' and resid 1147 through 1175
      removed outlier: 5.149A  pdb=" N   LEU A1171 " --> pdb=" O   GLY A1167 " (cutoff:3.500A)
      Proline residue:  A1172  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 154
      removed outlier: 3.674A  pdb=" N   ASN A 154 " --> pdb=" O   LEU A 366 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU A 366 " --> pdb=" O   ASN A 154 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 344
    Processing sheet with id=AA3, first strand: chain 'A' and resid 800 through 801
    Processing sheet with id=AA4, first strand: chain 'A' and resid 972 through 975

    407 hydrogen bonds defined for protein.
    1191 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.08

  Time building geometry restraints manager: 2.09 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1341
        1.33 -     1.45: 1835
        1.45 -     1.58: 4234
        1.58 -     1.70: 0
        1.70 -     1.82: 56
  Bond restraints: 7466
  Sorted by residual:
  bond pdb=" N   ILE A 342 "
       pdb=" CA  ILE A 342 "
    ideal  model  delta    sigma   weight residual
    1.456  1.504 -0.048 9.50e-03 1.11e+04 2.51e+01
  bond pdb=" N   VAL A 275 "
       pdb=" CA  VAL A 275 "
    ideal  model  delta    sigma   weight residual
    1.455  1.502 -0.047 1.04e-02 9.25e+03 2.05e+01
  bond pdb=" N   ASP A 260 "
       pdb=" CA  ASP A 260 "
    ideal  model  delta    sigma   weight residual
    1.455  1.484 -0.029 7.00e-03 2.04e+04 1.69e+01
  bond pdb=" N   ILE A 963 "
       pdb=" CA  ILE A 963 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 9.00e-03 1.23e+04 1.43e+01
  bond pdb=" N   GLY A 214 "
       pdb=" CA  GLY A 214 "
    ideal  model  delta    sigma   weight residual
    1.446  1.486 -0.040 1.06e-02 8.90e+03 1.39e+01
  ... (remaining 7461 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.82: 9789
        3.82 -     7.64: 372
        7.64 -    11.45: 8
       11.45 -    15.27: 1
       15.27 -    19.09: 2
  Bond angle restraints: 10172
  Sorted by residual:
  angle pdb=" N   SER A 415 "
        pdb=" CA  SER A 415 "
        pdb=" C   SER A 415 "
      ideal   model   delta    sigma   weight residual
     110.23   91.14   19.09 1.45e+00 4.76e-01 1.73e+02
  angle pdb=" N   LEU A 121 "
        pdb=" CA  LEU A 121 "
        pdb=" C   LEU A 121 "
      ideal   model   delta    sigma   weight residual
     108.69   93.01   15.68 1.77e+00 3.19e-01 7.85e+01
  angle pdb=" N   THR A 416 "
        pdb=" CA  THR A 416 "
        pdb=" C   THR A 416 "
      ideal   model   delta    sigma   weight residual
     112.45  101.16   11.29 1.39e+00 5.18e-01 6.60e+01
  angle pdb=" C   SER A 415 "
        pdb=" CA  SER A 415 "
        pdb=" CB  SER A 415 "
      ideal   model   delta    sigma   weight residual
     109.72  122.46  -12.74 1.66e+00 3.63e-01 5.89e+01
  angle pdb=" N   PRO A 252 "
        pdb=" CA  PRO A 252 "
        pdb=" CB  PRO A 252 "
      ideal   model   delta    sigma   weight residual
     103.08  110.31   -7.23 9.70e-01 1.06e+00 5.56e+01
  ... (remaining 10167 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.47: 4135
       21.47 -    42.93: 302
       42.93 -    64.40: 41
       64.40 -    85.86: 11
       85.86 -   107.33: 4
  Dihedral angle restraints: 4493
    sinusoidal: 1693
      harmonic: 2800
  Sorted by residual:
  dihedral pdb=" CA  SER A 313 "
           pdb=" C   SER A 313 "
           pdb=" N   THR A 314 "
           pdb=" CA  THR A 314 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.14  -35.86     0      5.00e+00 4.00e-02 5.14e+01
  dihedral pdb=" C   ALA A 246 "
           pdb=" N   ALA A 246 "
           pdb=" CA  ALA A 246 "
           pdb=" CB  ALA A 246 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -106.73  -15.87     0      2.50e+00 1.60e-01 4.03e+01
  dihedral pdb=" CA  HIS A 201 "
           pdb=" C   HIS A 201 "
           pdb=" N   LEU A 202 "
           pdb=" CA  LEU A 202 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.30   27.70     0      5.00e+00 4.00e-02 3.07e+01
  ... (remaining 4490 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.333: 1214
       0.333 -    0.666: 2
       0.666 -    0.999: 1
       0.999 -    1.332: 0
       1.332 -    1.665: 3
  Chirality restraints: 1220
  Sorted by residual:
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.73   -1.67 2.00e-02 2.50e+03 6.93e+03
  chirality pdb=" C1  NAG E   2 "
            pdb=" O4  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.96   -1.44 2.00e-02 2.50e+03 5.18e+03
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.05   -1.35 2.00e-02 2.50e+03 4.53e+03
  ... (remaining 1217 not shown)

  Planarity restraints: 1279
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A1000 "   -0.263 2.00e-02 2.50e+03   2.50e-01 7.83e+02
        pdb=" CG  ASN A1000 "    0.078 2.00e-02 2.50e+03
        pdb=" OD1 ASN A1000 "    0.080 2.00e-02 2.50e+03
        pdb=" ND2 ASN A1000 "    0.389 2.00e-02 2.50e+03
        pdb=" C1  NAG E   1 "   -0.283 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 229 "    0.018 2.00e-02 2.50e+03   3.67e-02 1.35e+01
        pdb=" C   ILE A 229 "   -0.064 2.00e-02 2.50e+03
        pdb=" O   ILE A 229 "    0.024 2.00e-02 2.50e+03
        pdb=" N   THR A 230 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 156 "    0.014 2.00e-02 2.50e+03   2.94e-02 8.66e+00
        pdb=" C   GLN A 156 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   GLN A 156 "    0.019 2.00e-02 2.50e+03
        pdb=" N   LEU A 157 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1276 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 168
        2.71 -     3.25: 7011
        3.25 -     3.80: 11318
        3.80 -     4.35: 14002
        4.35 -     4.90: 23666
  Nonbonded interactions: 56165
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 141 "
            pdb=" C1  NAG B   1 "
     model   vdw
     2.157 3.550
  nonbonded pdb=" ND2 ASN A 414 "
            pdb=" O5  NAG D   1 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" ND2 ASN A 414 "
            pdb=" C2  NAG D   1 "
     model   vdw
     2.396 3.550
  nonbonded pdb=" O   GLY A1129 "
            pdb=" OG  SER A1132 "
     model   vdw
     2.397 3.040
  nonbonded pdb=" O   SER A 799 "
            pdb=" OG  SER A 799 "
     model   vdw
     2.399 3.040
  ... (remaining 56160 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.910
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6342
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      :  0.014   0.062   7466  Z= 0.941
  Angle     :  1.882  19.090  10172  Z= 1.393
  Chirality :  0.112   1.665   1220
  Planarity :  0.005   0.037   1278
  Dihedral  : 15.735 107.325   2685
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.33 %
    Favored  : 89.56 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 12.36 %
    Favored  : 86.79 %
  Cbeta Deviations :  0.33 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.81 (0.22), residues: 958
  helix: -1.66 (0.18), residues: 542
  sheet: -2.05 (0.71), residues: 43
  loop : -3.88 (0.26), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP A 337 
 HIS   0.009   0.002   HIS A 950 
 PHE   0.035   0.003   PHE A 757 
 TYR   0.029   0.003   TYR A1001 
 ARG   0.010   0.001   ARG A 995 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 174
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 ASP cc_start: 0.7103 (t0) cc_final: 0.6897 (t0)
REVERT: A  520 HIS cc_start: 0.7256 (t70) cc_final: 0.6119 (m-70)
REVERT: A  755 PHE cc_start: 0.6989 (t80) cc_final: 0.6789 (t80)
REVERT: A  979 ASN cc_start: 0.7621 (t0) cc_final: 0.6993 (t0)
REVERT: A 1004 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7130 (tp)
REVERT: A 1066 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6792 (mt-10)
REVERT: A 1105 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6432 (pt)
  outliers start: 6
  outliers final: 1
  residues processed: 180
  average time/residue: 0.2204
  time to fit residues: 52.2483
Evaluate side-chains
  121 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 118
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1105 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 75 optimal weight:    0.4980
   chunk 29 optimal weight:    2.9990
   chunk 45 optimal weight:    0.4980
   chunk 56 optimal weight:    0.9980
   chunk 87 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 124 ASN
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 177 GLN
A 312 ASN
A 527 GLN
A1166 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.202974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.177193 restraints weight = 10078.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.181972 restraints weight = 5994.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.184157 restraints weight = 3720.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.4132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6700
moved from start:          0.1844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7466  Z= 0.205
  Angle     :  0.711  10.994  10172  Z= 0.358
  Chirality :  0.044   0.316   1220
  Planarity :  0.005   0.045   1278
  Dihedral  :  9.596  80.751   1198
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 19.18 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.29 (0.26), residues: 958
  helix: -0.41 (0.21), residues: 563
  sheet: -1.56 (0.76), residues: 43
  loop : -3.37 (0.29), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 863 
 HIS   0.005   0.001   HIS A 950 
 PHE   0.031   0.002   PHE A 798 
 TYR   0.010   0.001   TYR A 740 
 ARG   0.005   0.001   ARG A 603 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 LYS cc_start: 0.3429 (tptt) cc_final: 0.2900 (mmtm)
REVERT: A  154 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8477 (p0)
REVERT: A  158 MET cc_start: 0.7969 (ttp) cc_final: 0.7575 (ttm)
REVERT: A  373 TYR cc_start: 0.7246 (t80) cc_final: 0.6301 (t80)
REVERT: A  602 ARG cc_start: 0.5068 (mmt180) cc_final: 0.3162 (ptp-170)
REVERT: A  789 ASP cc_start: 0.6643 (m-30) cc_final: 0.6241 (m-30)
REVERT: A 1086 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7319 (mm)
  outliers start: 17
  outliers final: 8
  residues processed: 142
  average time/residue: 0.1620
  time to fit residues: 33.1244
Evaluate side-chains
  126 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 ASN
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue 1086 LEU
Chi-restraints excluded: chain A residue 1117 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 54 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 154 ASN
A 361 GLN
A 520 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.202388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.177840 restraints weight = 10419.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.181071 restraints weight = 6428.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.182594 restraints weight = 4478.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.4132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6710
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7466  Z= 0.192
  Angle     :  0.642  10.823  10172  Z= 0.322
  Chirality :  0.043   0.356   1220
  Planarity :  0.005   0.050   1278
  Dihedral  :  7.959  58.020   1193
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 21.31 %
    Favored  : 75.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.27), residues: 958
  helix:  0.10 (0.21), residues: 574
  sheet: -1.33 (0.78), residues: 43
  loop : -3.07 (0.31), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 863 
 HIS   0.016   0.001   HIS A 520 
 PHE   0.025   0.002   PHE A 798 
 TYR   0.018   0.001   TYR A 452 
 ARG   0.005   0.000   ARG A  80 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 LYS cc_start: 0.3277 (tptt) cc_final: 0.2962 (mmtm)
REVERT: A  158 MET cc_start: 0.7959 (ttp) cc_final: 0.7562 (ttm)
REVERT: A  372 MET cc_start: 0.8568 (tpp) cc_final: 0.8092 (ttm)
REVERT: A  373 TYR cc_start: 0.7269 (t80) cc_final: 0.6259 (t80)
REVERT: A  602 ARG cc_start: 0.4837 (mmt180) cc_final: 0.2914 (ptp-170)
REVERT: A  789 ASP cc_start: 0.6891 (m-30) cc_final: 0.6567 (m-30)
REVERT: A 1076 ILE cc_start: 0.8570 (mm) cc_final: 0.8368 (mt)
  outliers start: 23
  outliers final: 13
  residues processed: 144
  average time/residue: 0.1578
  time to fit residues: 32.7478
Evaluate side-chains
  129 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  739 HIS
Chi-restraints excluded: chain A residue  843 MET
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1117 LEU
Chi-restraints excluded: chain A residue 1121 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 93 optimal weight:    3.9990
   chunk 79 optimal weight:    0.3980
   chunk 4 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 54 optimal weight:   10.0000
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.199451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.175517 restraints weight = 10776.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.179890 restraints weight = 6636.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.180899 restraints weight = 4221.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.4101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6755
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7466  Z= 0.202
  Angle     :  0.644   9.929  10172  Z= 0.318
  Chirality :  0.043   0.343   1220
  Planarity :  0.005   0.069   1278
  Dihedral  :  7.493  58.765   1193
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 23.44 %
    Favored  : 72.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.27), residues: 958
  helix:  0.31 (0.22), residues: 574
  sheet: -0.94 (0.81), residues: 45
  loop : -2.96 (0.31), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 863 
 HIS   0.012   0.001   HIS A 520 
 PHE   0.039   0.002   PHE A 798 
 TYR   0.019   0.001   TYR A 452 
 ARG   0.004   0.000   ARG A  80 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 117
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 LYS cc_start: 0.3536 (tptt) cc_final: 0.3269 (mmtm)
REVERT: A  158 MET cc_start: 0.7963 (ttp) cc_final: 0.7575 (ttm)
REVERT: A  373 TYR cc_start: 0.7205 (t80) cc_final: 0.6113 (t80)
REVERT: A  602 ARG cc_start: 0.4835 (mmt180) cc_final: 0.2957 (ptp-170)
REVERT: A  789 ASP cc_start: 0.6799 (m-30) cc_final: 0.6527 (m-30)
REVERT: A 1086 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.6909 (mp)
  outliers start: 27
  outliers final: 19
  residues processed: 136
  average time/residue: 0.1560
  time to fit residues: 30.4512
Evaluate side-chains
  133 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  279 GLU
Chi-restraints excluded: chain A residue  346 THR
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  739 HIS
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  843 MET
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1086 LEU
Chi-restraints excluded: chain A residue 1094 VAL
Chi-restraints excluded: chain A residue 1117 LEU
Chi-restraints excluded: chain A residue 1121 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 70 optimal weight:    0.4980
   chunk 47 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 91 optimal weight:    0.8980
   chunk 38 optimal weight:    5.9990
   chunk 90 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0060
   chunk 87 optimal weight:    0.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.199918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.177375 restraints weight = 10557.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.180093 restraints weight = 6350.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.182510 restraints weight = 4344.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.4136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6710
moved from start:          0.3031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7466  Z= 0.161
  Angle     :  0.624  11.488  10172  Z= 0.303
  Chirality :  0.042   0.387   1220
  Planarity :  0.005   0.058   1278
  Dihedral  :  7.314  55.222   1193
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 23.15 %
    Favored  : 72.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.27), residues: 958
  helix:  0.52 (0.22), residues: 576
  sheet: -0.76 (0.82), residues: 45
  loop : -2.88 (0.31), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 863 
 HIS   0.010   0.001   HIS A 520 
 PHE   0.024   0.001   PHE A 798 
 TYR   0.021   0.001   TYR A 452 
 ARG   0.007   0.000   ARG A  80 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 126
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
REVERT: A  156 GLN cc_start: 0.8669 (mp10) cc_final: 0.8457 (mp10)
REVERT: A  158 MET cc_start: 0.7969 (ttp) cc_final: 0.7623 (ttm)
REVERT: A  373 TYR cc_start: 0.7022 (t80) cc_final: 0.6080 (t80)
REVERT: A  602 ARG cc_start: 0.4815 (mmt180) cc_final: 0.2684 (ptp-170)
REVERT: A  789 ASP cc_start: 0.6568 (m-30) cc_final: 0.6330 (m-30)
REVERT: A 1086 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6820 (mt)
  outliers start: 28
  outliers final: 20
  residues processed: 145
  average time/residue: 0.1674
  time to fit residues: 34.0040
Evaluate side-chains
  135 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  374 GLU
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  739 HIS
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  843 MET
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1016 LEU
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1086 LEU
Chi-restraints excluded: chain A residue 1094 VAL
Chi-restraints excluded: chain A residue 1117 LEU
Chi-restraints excluded: chain A residue 1121 HIS
Chi-restraints excluded: chain A residue 1137 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 46 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 30 optimal weight:   10.0000
   chunk 42 optimal weight:    0.1980
   chunk 93 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0980
   chunk 12 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 28 optimal weight:    7.9990
   chunk 72 optimal weight:    4.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 177 GLN
** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 HIS
A1166 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.200416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.178183 restraints weight = 10527.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.180908 restraints weight = 6301.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.183315 restraints weight = 4330.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.4142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6700
moved from start:          0.3246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7466  Z= 0.162
  Angle     :  0.614  12.409  10172  Z= 0.299
  Chirality :  0.042   0.400   1220
  Planarity :  0.004   0.051   1278
  Dihedral  :  6.695  54.447   1193
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 24.29 %
    Favored  : 71.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.27), residues: 958
  helix:  0.72 (0.22), residues: 576
  sheet: -0.78 (0.81), residues: 45
  loop : -2.79 (0.32), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 863 
 HIS   0.009   0.001   HIS A 520 
 PHE   0.023   0.001   PHE A 798 
 TYR   0.020   0.001   TYR A 452 
 ARG   0.005   0.000   ARG A 401 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 117
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
REVERT: A  158 MET cc_start: 0.7950 (ttp) cc_final: 0.7571 (ttm)
REVERT: A  373 TYR cc_start: 0.7023 (t80) cc_final: 0.6062 (t80)
REVERT: A  575 LEU cc_start: 0.7857 (mm) cc_final: 0.7629 (mm)
REVERT: A  602 ARG cc_start: 0.4726 (mmt180) cc_final: 0.2563 (ptp-170)
REVERT: A 1086 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6849 (mp)
REVERT: A 1166 ASN cc_start: 0.7718 (OUTLIER) cc_final: 0.7390 (t0)
  outliers start: 30
  outliers final: 19
  residues processed: 140
  average time/residue: 0.1545
  time to fit residues: 30.9760
Evaluate side-chains
  130 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  374 GLU
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  739 HIS
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1086 LEU
Chi-restraints excluded: chain A residue 1094 VAL
Chi-restraints excluded: chain A residue 1117 LEU
Chi-restraints excluded: chain A residue 1121 HIS
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1166 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 71 optimal weight:    3.9990
   chunk 16 optimal weight:   10.0000
   chunk 22 optimal weight:    0.0170
   chunk 93 optimal weight:    0.0030
   overall best weight:    0.4830

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 HIS
A1166 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.201120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.177399 restraints weight = 10463.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.180442 restraints weight = 6603.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.182200 restraints weight = 4625.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.4128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6714
moved from start:          0.3397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7466  Z= 0.162
  Angle     :  0.632  13.961  10172  Z= 0.304
  Chirality :  0.042   0.412   1220
  Planarity :  0.005   0.075   1278
  Dihedral  :  6.555  54.404   1193
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 25.14 %
    Favored  : 70.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.27), residues: 958
  helix:  0.77 (0.22), residues: 577
  sheet: -0.63 (0.82), residues: 45
  loop : -2.78 (0.32), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 948 
 HIS   0.010   0.001   HIS A 520 
 PHE   0.019   0.001   PHE A 798 
 TYR   0.019   0.001   TYR A 452 
 ARG   0.008   0.000   ARG A 144 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 113
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  158 MET cc_start: 0.7920 (ttp) cc_final: 0.7567 (ttm)
REVERT: A  373 TYR cc_start: 0.7090 (t80) cc_final: 0.6235 (t80)
REVERT: A  598 MET cc_start: 0.7659 (mmp) cc_final: 0.7183 (mmt)
REVERT: A  602 ARG cc_start: 0.4798 (mmt180) cc_final: 0.2549 (ptp-170)
REVERT: A 1086 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6904 (mt)
REVERT: A 1166 ASN cc_start: 0.7721 (OUTLIER) cc_final: 0.7513 (t0)
  outliers start: 30
  outliers final: 24
  residues processed: 132
  average time/residue: 0.1701
  time to fit residues: 32.1210
Evaluate side-chains
  132 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 106
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  374 GLU
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  843 MET
Chi-restraints excluded: chain A residue  924 THR
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1016 LEU
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1086 LEU
Chi-restraints excluded: chain A residue 1094 VAL
Chi-restraints excluded: chain A residue 1117 LEU
Chi-restraints excluded: chain A residue 1121 HIS
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1166 ASN
Chi-restraints excluded: chain A residue 1168 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 88 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0470
   chunk 71 optimal weight:    0.4980
   chunk 68 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9990
   chunk 22 optimal weight:    0.3980
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 HIS
A 802 ASN
A1166 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.201000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.178248 restraints weight = 10590.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.181086 restraints weight = 6462.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.182647 restraints weight = 4573.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6697
moved from start:          0.3533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7466  Z= 0.161
  Angle     :  0.634  14.298  10172  Z= 0.302
  Chirality :  0.042   0.448   1220
  Planarity :  0.005   0.064   1278
  Dihedral  :  6.383  54.286   1193
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 25.57 %
    Favored  : 69.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.28), residues: 958
  helix:  0.89 (0.22), residues: 575
  sheet: -0.52 (0.83), residues: 43
  loop : -2.72 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 948 
 HIS   0.009   0.001   HIS A 520 
 PHE   0.018   0.001   PHE A 798 
 TYR   0.020   0.001   TYR A 452 
 ARG   0.007   0.000   ARG A  80 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 106
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  158 MET cc_start: 0.7933 (ttp) cc_final: 0.7582 (ttm)
REVERT: A  365 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8434 (mp10)
REVERT: A  373 TYR cc_start: 0.7023 (t80) cc_final: 0.6234 (t80)
REVERT: A  598 MET cc_start: 0.7572 (mmp) cc_final: 0.7296 (mmp)
REVERT: A  602 ARG cc_start: 0.4614 (mmt180) cc_final: 0.2467 (ptp-170)
REVERT: A 1086 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6940 (mt)
  outliers start: 33
  outliers final: 25
  residues processed: 129
  average time/residue: 0.1581
  time to fit residues: 29.3334
Evaluate side-chains
  130 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  365 GLN
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  374 GLU
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  739 HIS
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  800 PHE
Chi-restraints excluded: chain A residue  802 ASN
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1016 LEU
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1086 LEU
Chi-restraints excluded: chain A residue 1094 VAL
Chi-restraints excluded: chain A residue 1117 LEU
Chi-restraints excluded: chain A residue 1121 HIS
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1166 ASN
Chi-restraints excluded: chain A residue 1168 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 15 optimal weight:    6.9990
   chunk 70 optimal weight:    0.0670
   chunk 46 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 68 optimal weight:    0.7980
   chunk 82 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.6920

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 HIS
A 802 ASN
A1166 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.202129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.178328 restraints weight = 10596.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.181338 restraints weight = 6700.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.183281 restraints weight = 4578.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.4131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6714
moved from start:          0.3588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7466  Z= 0.173
  Angle     :  0.638  15.231  10172  Z= 0.305
  Chirality :  0.043   0.449   1220
  Planarity :  0.005   0.060   1278
  Dihedral  :  6.301  54.076   1193
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 25.28 %
    Favored  : 69.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.28), residues: 958
  helix:  0.91 (0.22), residues: 578
  sheet: -0.45 (0.82), residues: 43
  loop : -2.75 (0.32), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1027 
 HIS   0.010   0.001   HIS A 520 
 PHE   0.017   0.001   PHE A 798 
 TYR   0.019   0.001   TYR A 452 
 ARG   0.007   0.000   ARG A  80 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 104
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
REVERT: A  158 MET cc_start: 0.7909 (ttp) cc_final: 0.7542 (ttm)
REVERT: A  365 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8367 (mp10)
REVERT: A  373 TYR cc_start: 0.7052 (t80) cc_final: 0.6219 (t80)
REVERT: A  575 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7350 (mm)
REVERT: A  598 MET cc_start: 0.7597 (mmp) cc_final: 0.7265 (mmp)
REVERT: A  602 ARG cc_start: 0.4460 (mmt180) cc_final: 0.2270 (ptp-170)
REVERT: A 1086 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6973 (mt)
  outliers start: 34
  outliers final: 28
  residues processed: 128
  average time/residue: 0.1649
  time to fit residues: 30.3461
Evaluate side-chains
  132 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 101
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  365 GLN
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  374 GLU
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  575 LEU
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  739 HIS
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  806 VAL
Chi-restraints excluded: chain A residue  843 MET
Chi-restraints excluded: chain A residue 1004 LEU
Chi-restraints excluded: chain A residue 1016 LEU
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1086 LEU
Chi-restraints excluded: chain A residue 1094 VAL
Chi-restraints excluded: chain A residue 1117 LEU
Chi-restraints excluded: chain A residue 1121 HIS
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1168 LEU
Chi-restraints excluded: chain A residue 1171 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 82 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:   10.0000
   chunk 49 optimal weight:    6.9990
   chunk 17 optimal weight:    7.9990
   chunk 7 optimal weight:    0.7980
   chunk 73 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 HIS
A1166 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.200750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.176481 restraints weight = 11066.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.179117 restraints weight = 7447.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.180941 restraints weight = 5205.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.4113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6758
moved from start:          0.3671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   7466  Z= 0.189
  Angle     :  0.648  15.617  10172  Z= 0.312
  Chirality :  0.044   0.466   1220
  Planarity :  0.005   0.058   1278
  Dihedral  :  6.234  53.679   1193
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 25.28 %
    Favored  : 70.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.28), residues: 958
  helix:  0.95 (0.22), residues: 576
  sheet: -0.44 (0.82), residues: 43
  loop : -2.81 (0.31), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.074   0.003   TRP A 948 
 HIS   0.010   0.001   HIS A 520 
 PHE   0.018   0.001   PHE A 798 
 TYR   0.020   0.001   TYR A 452 
 ARG   0.007   0.000   ARG A  80 

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 104
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  158 MET cc_start: 0.8010 (ttp) cc_final: 0.7667 (ttm)
REVERT: A  365 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8393 (mp10)
REVERT: A  373 TYR cc_start: 0.6773 (t80) cc_final: 0.6072 (t80)
REVERT: A  575 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7482 (mm)
REVERT: A  598 MET cc_start: 0.7569 (mmp) cc_final: 0.7337 (mmp)
REVERT: A  602 ARG cc_start: 0.4315 (mmt180) cc_final: 0.2224 (ptp-170)
REVERT: A 1086 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7034 (mt)
  outliers start: 33
  outliers final: 27
  residues processed: 127
  average time/residue: 0.1568
  time to fit residues: 28.7768
Evaluate side-chains
  133 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 103
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  365 GLN
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  374 GLU
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  575 LEU
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  739 HIS
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  806 VAL
Chi-restraints excluded: chain A residue  843 MET
Chi-restraints excluded: chain A residue 1016 LEU
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1086 LEU
Chi-restraints excluded: chain A residue 1094 VAL
Chi-restraints excluded: chain A residue 1117 LEU
Chi-restraints excluded: chain A residue 1121 HIS
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1166 ASN
Chi-restraints excluded: chain A residue 1168 LEU
Chi-restraints excluded: chain A residue 1171 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 4 optimal weight:    0.4980
   chunk 18 optimal weight:    9.9990
   chunk 50 optimal weight:    0.8980
   chunk 16 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0030
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.6592

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 HIS
A1166 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.200940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.177500 restraints weight = 10814.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.180592 restraints weight = 6717.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.181901 restraints weight = 4797.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.4123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6735
moved from start:          0.3735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7466  Z= 0.170
  Angle     :  0.636  15.683  10172  Z= 0.305
  Chirality :  0.043   0.445   1220
  Planarity :  0.004   0.056   1278
  Dihedral  :  6.158  53.575   1193
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 25.71 %
    Favored  : 69.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.28), residues: 958
  helix:  1.02 (0.22), residues: 576
  sheet: -0.34 (0.82), residues: 43
  loop : -2.78 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP A 948 
 HIS   0.010   0.001   HIS A 520 
 PHE   0.018   0.001   PHE A 798 
 TYR   0.020   0.001   TYR A 452 
 ARG   0.007   0.000   ARG A  80 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2258.86 seconds
wall clock time: 41 minutes 21.18 seconds (2481.18 seconds total)