Starting phenix.real_space_refine
on Sat Aug 23 22:04:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t60_41062/08_2025/8t60_41062.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t60_41062/08_2025/8t60_41062.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t60_41062/08_2025/8t60_41062.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t60_41062/08_2025/8t60_41062.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t60_41062/08_2025/8t60_41062.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t60_41062/08_2025/8t60_41062.map"
  }
  resolution = 3.29
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 126 atoms to isotropic.
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: 6
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     Na      1      4.78       5
     C    4855      2.51       5
     N    1216      2.21       5
     O    1397      1.98       5
     H    7418      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14921
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 6537
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 417, 6516
          Classifications: {'peptide': 417}
          Link IDs: {'PTRANS': 12, 'TRANS': 404}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 26
      Conformer: "B"
        Number of residues, atoms: 417, 6516
          Classifications: {'peptide': 417}
          Link IDs: {'PTRANS': 12, 'TRANS': 404}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 26
          bond proxies already assigned to first conformer: 6574
    Chain: "B"
      Number of atoms: 1832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 1832
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 5, 'TRANS': 116}
    Chain: "H"
      Number of atoms: 3396
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 3396
          Classifications: {'peptide': 229}
          Link IDs: {'PTRANS': 11, 'TRANS': 217}
    Chain: "L"
      Number of atoms: 3155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 3155
          Classifications: {'peptide': 210}
          Link IDs: {'PTRANS': 10, 'TRANS': 199}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' NA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.48, per 1000 atoms: 0.30
  Number of scatterers: 14921
  At special positions: 0
  Unit cell: (68.8, 83.42, 173.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      34     16.00
     Na      1     11.00
     O    1397      8.00
     N    1216      7.00
     C    4855      6.00
     H    7418      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 140 " - pdb=" SG  CYS H 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.30
  Conformation dependent library (CDL) restraints added in 574.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1796

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 14 sheets defined
      39.7% alpha, 22.4% 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 4 through 36
      removed outlier: 3.522A  pdb=" N   LYS A   8 " --> pdb=" O   SER A   4 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ALA A  15 " --> pdb=" O   TYR A  11 " (cutoff:3.500A)
      removed outlier: 4.962A  pdb=" N   ILE A  24 " --> pdb=" O   PHE A  20 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   VAL A  25 " --> pdb=" O   ALA A  21 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   LEU A  29 " --> pdb=" O   VAL A  25 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   MET A  30 " --> pdb=" O   TYR A  26 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   TYR A  31 " --> pdb=" O   MET A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 58
      removed outlier: 3.895A  pdb=" N   ASP A  55 " --> pdb=" O   ALA A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 69
      removed outlier: 4.134A  pdb=" N   MET A  62 " --> pdb=" O   ASN A  58 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLY A  63 " --> pdb=" O   ASP A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 95
      removed outlier: 3.587A  pdb=" N   LEU A  85 " --> pdb=" O   LEU A  81 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   PHE A  95 " --> pdb=" O   LEU A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 100
      removed outlier: 3.556A  pdb=" N   PHE A 100 " --> pdb=" O   ALA A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 134
      removed outlier: 4.241A  pdb=" N   VAL A 106 " --> pdb=" O   GLY A 102 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   VAL A 107 " --> pdb=" O   THR A 103 " (cutoff:3.500A)
      Proline residue:  A 126  - end of helix
      removed outlier: 4.745A  pdb=" N   VAL A 131 " --> pdb=" O   PHE A 127 " (cutoff:3.500A)
      Proline residue:  A 132  - end of helix
    Processing helix  chain 'A' and resid 140 through 145
      removed outlier: 3.558A  pdb=" N   LEU A 144 " --> pdb=" O   GLU A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 171
      removed outlier: 3.769A  pdb=" N   ARG A 149 " --> pdb=" O   VAL A 145 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   PHE A 151 " --> pdb=" O   PHE A 147 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLY A 156 " --> pdb=" O   ALA A 152 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   PHE A 157 " --> pdb=" O   SER A 153 " (cutoff:3.500A)
      removed outlier: 5.290A  pdb=" N   LEU A 164 " --> pdb=" O   ALA A 160 " (cutoff:3.500A)
      Proline residue:  A 165  - end of helix
    Processing helix  chain 'A' and resid 176 through 200
      removed outlier: 3.672A  pdb=" N   MET A 181 " --> pdb=" O   PHE A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 230
    Processing helix  chain 'A' and resid 230 through 261
      removed outlier: 3.563A  pdb=" N   ALA A 242 " --> pdb=" O   GLY A 238 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   TYR A 243 " --> pdb=" O   MET A 239 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA A 254 " --> pdb=" O   ILE A 250 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   ILE A 255 " --> pdb=" O   ASN A 251 " (cutoff:3.500A)
      removed outlier: 5.452A  pdb=" N   TYR A 256 " --> pdb=" O   GLY A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 273
    Processing helix  chain 'A' and resid 274 through 285
      removed outlier: 4.058A  pdb=" N   ALA A 278 " --> pdb=" O   TYR A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 293
    Processing helix  chain 'A' and resid 294 through 317
      Proline residue:  A 306  - end of helix
    Processing helix  chain 'A' and resid 323 through 355
      removed outlier: 4.361A  pdb=" N   VAL A 346 " --> pdb=" O   TRP A 342 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   ILE A 347 " --> pdb=" O   VAL A 343 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   MET A 348 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   VAL A 349 " --> pdb=" O   GLN A 345 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   ALA A 350 " --> pdb=" O   VAL A 346 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ASP A 351 " --> pdb=" O   ILE A 347 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   TYR A 355 " --> pdb=" O   ASP A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 395
      removed outlier: 3.669A  pdb=" N   SER A 370 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   VAL A 371 " --> pdb=" O   ILE A 367 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   GLN A 372 " --> pdb=" O   ALA A 368 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   THR A 373 " --> pdb=" O   TYR A 369 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ILE A 394 " --> pdb=" O   VAL A 390 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   GLY A 395 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 417
    Processing helix  chain 'A' and resid 417 through 432
      removed outlier: 3.853A  pdb=" N   PHE A 421 " --> pdb=" O   LEU A 417 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   TYR A 432 " --> pdb=" O   LEU A 428 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 64
    Processing helix  chain 'B' and resid 86 through 90
    Processing helix  chain 'H' and resid 61 through 64
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 3.697A  pdb=" N   ASP H  86 " --> pdb=" O   ARG H  83 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   THR H  87 " --> pdb=" O   ALA H  84 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 83 through 87'
    Processing helix  chain 'L' and resid 183 through 187
      removed outlier: 3.685A  pdb=" N   GLU L 187 " --> pdb=" O   LYS L 183 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 183 through 187'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 6
      removed outlier: 3.572A  pdb=" N   SER B  25 " --> pdb=" O   GLN B   3 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   VAL B  78 " --> pdb=" O   CYS B  22 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 59
      removed outlier: 6.627A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   THR B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   MET B  34 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.787A  pdb=" N   GLN H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   THR H  77 " --> pdb=" O   ASP H  72 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.850A  pdb=" N   GLY H  10 " --> pdb=" O   LEU H 108 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   THR H 110 " --> pdb=" O   GLY H  10 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   ILE H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   TYR H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 121 through 124
      removed outlier: 4.428A  pdb=" N   GLY H 139 " --> pdb=" O   LEU H 124 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 121 through 124
      removed outlier: 4.428A  pdb=" N   GLY H 139 " --> pdb=" O   LEU H 124 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 151 through 154
      removed outlier: 3.995A  pdb=" N   THR H 205 " --> pdb=" O   HIS H 200 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 151 through 154
      removed outlier: 4.407A  pdb=" N   TYR H 194 " --> pdb=" O   VAL H 211 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.508A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'L' and resid 19 through 23
      removed outlier: 3.680A  pdb=" N   THR L  72 " --> pdb=" O   SER L  65 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 45 through 48
      removed outlier: 6.605A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 89 through 90
      removed outlier: 3.538A  pdb=" N   THR L  97 " --> pdb=" O   GLN L  90 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 114 through 118
      removed outlier: 3.583A  pdb=" N   VAL L 133 " --> pdb=" O   PHE L 118 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 153 through 154

    385 hydrogen bonds defined for protein.
    1076 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.34

  Time building geometry restraints manager: 1.82 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 7414
        1.03 -     1.23: 47
        1.23 -     1.43: 3272
        1.43 -     1.62: 4321
        1.62 -     1.82: 54
  Bond restraints: 15108
  Sorted by residual:
  bond pdb=" N   GLU H   1 "
       pdb=" CA  GLU H   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.81e+00
  bond pdb=" N   GLU H   1 "
       pdb=" H   GLU H   1 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.30e+00
  bond pdb=" C   THR A 121 "
       pdb=" O   THR A 121 "
    ideal  model  delta    sigma   weight residual
    1.236  1.247 -0.010 1.15e-02 7.56e+03 8.12e-01
  bond pdb=" C   VAL A 185 "
       pdb=" O   VAL A 185 "
    ideal  model  delta    sigma   weight residual
    1.237  1.246 -0.009 1.17e-02 7.31e+03 6.03e-01
  bond pdb=" N   ILE A 125 "
       pdb=" CA  ILE A 125 "
    ideal  model  delta    sigma   weight residual
    1.463  1.472 -0.009 1.20e-02 6.94e+03 5.33e-01
  ... (remaining 15103 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 25209
        0.98 -     1.97: 1861
        1.97 -     2.95: 91
        2.95 -     3.94: 39
        3.94 -     4.92: 9
  Bond angle restraints: 27209
  Sorted by residual:
  angle pdb=" N   GLY A 395 "
        pdb=" CA  GLY A 395 "
        pdb=" C   GLY A 395 "
      ideal   model   delta    sigma   weight residual
     111.12  115.25   -4.13 1.49e+00 4.50e-01 7.67e+00
  angle pdb=" N   ASP A 124 "
        pdb=" CA  ASP A 124 "
        pdb=" C   ASP A 124 "
      ideal   model   delta    sigma   weight residual
     111.69  114.17   -2.48 1.23e+00 6.61e-01 4.08e+00
  angle pdb=" CA  GLY B 107 "
        pdb=" C   GLY B 107 "
        pdb=" N   LYS B 108 "
      ideal   model   delta    sigma   weight residual
     114.61  117.12   -2.51 1.26e+00 6.30e-01 3.98e+00
  angle pdb=" N   ARG A 139 "
        pdb=" CA  ARG A 139 "
        pdb=" CB  ARG A 139 "
      ideal   model   delta    sigma   weight residual
     113.65  110.82    2.83 1.47e+00 4.63e-01 3.71e+00
  angle pdb=" N   ALA A 173 "
        pdb=" CA  ALA A 173 "
        pdb=" CB  ALA A 173 "
      ideal   model   delta    sigma   weight residual
     113.65  110.95    2.70 1.47e+00 4.63e-01 3.38e+00
  ... (remaining 27204 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.61: 6656
       16.61 -    33.23: 373
       33.23 -    49.84: 123
       49.84 -    66.45: 63
       66.45 -    83.06: 4
  Dihedral angle restraints: 7219
    sinusoidal: 3778
      harmonic: 3441
  Sorted by residual:
  dihedral pdb=" CA  LEU A 130 "
           pdb=" C   LEU A 130 "
           pdb=" N   VAL A 131 "
           pdb=" CA  VAL A 131 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.94  -17.06     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CA  LEU A 393 "
           pdb=" C   LEU A 393 "
           pdb=" N   ILE A 394 "
           pdb=" CA  ILE A 394 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.39  -16.61     0      5.00e+00 4.00e-02 1.10e+01
  dihedral pdb=" CA  VAL H 142 "
           pdb=" C   VAL H 142 "
           pdb=" N   LYS H 143 "
           pdb=" CA  LYS H 143 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.01  -15.99     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 7216 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 776
       0.031 -    0.061: 285
       0.061 -    0.092: 73
       0.092 -    0.123: 59
       0.123 -    0.153: 6
  Chirality restraints: 1199
  Sorted by residual:
  chirality pdb=" CA  ILE L  48 "
            pdb=" N   ILE L  48 "
            pdb=" C   ILE L  48 "
            pdb=" CB  ILE L  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.89e-01
  chirality pdb=" CA  VAL H  37 "
            pdb=" N   VAL H  37 "
            pdb=" C   VAL H  37 "
            pdb=" CB  VAL H  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.58e-01
  chirality pdb=" CA  VAL A 204 "
            pdb=" N   VAL A 204 "
            pdb=" C   VAL A 204 "
            pdb=" CB  VAL A 204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.50e-01
  ... (remaining 1196 not shown)

  Planarity restraints: 2238
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 164 "    0.015 5.00e-02 4.00e+02   2.31e-02 8.53e-01
        pdb=" N   PRO A 165 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO A 165 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 165 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA H 125 "    0.015 5.00e-02 4.00e+02   2.25e-02 8.07e-01
        pdb=" N   PRO H 126 "   -0.039 5.00e-02 4.00e+02
        pdb=" CA  PRO H 126 "    0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO H 126 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L  49 "   -0.009 2.00e-02 2.50e+03   5.16e-03 8.00e-01
        pdb=" CG  TYR L  49 "    0.015 2.00e-02 2.50e+03
        pdb=" CD1 TYR L  49 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR L  49 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR L  49 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR L  49 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR L  49 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR L  49 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD1 TYR L  49 "    0.001 2.00e-02 2.50e+03
        pdb=" HD2 TYR L  49 "    0.000 2.00e-02 2.50e+03
        pdb=" HE1 TYR L  49 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE2 TYR L  49 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 2235 not shown)

  Histogram of nonbonded interaction distances:
        1.67 -     2.26: 1835
        2.26 -     2.84: 33084
        2.84 -     3.43: 36041
        3.43 -     4.01: 49785
        4.01 -     4.60: 76207
  Nonbonded interactions: 196952
  Sorted by model distance:
  nonbonded pdb=" HH  TYR L  36 "
            pdb=" OE1 GLN L  89 "
     model   vdw
     1.673 2.450
  nonbonded pdb=" O   THR A 159 "
            pdb=" HG1 THR A 163 "
     model   vdw
     1.693 2.450
  nonbonded pdb=" OD2 ASP L 151 "
            pdb=" HD1 HIS L 189 "
     model   vdw
     1.708 2.450
  nonbonded pdb=" OH  TYR A  32 "
            pdb=" HD1 HIS A  98 "
     model   vdw
     1.720 2.450
  nonbonded pdb=" O   ASP L  82 "
            pdb=" HH  TYR L  86 "
     model   vdw
     1.722 2.450
  ... (remaining 196947 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=0.48 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:             4.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.100
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     17.340
  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:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7695  Z= 0.135
  Angle     :  0.510   4.922  10484  Z= 0.282
  Chirality :  0.040   0.153   1199
  Planarity :  0.003   0.024   1303
  Dihedral  : 11.070  81.545   2655
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  8.14 %
    Favored  : 90.01 %
  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 aren not related in a simple way.
  whole:  0.46 (0.28), residues: 967
  helix:  2.23 (0.29), residues: 340
  sheet:  0.60 (0.37), residues: 224
  loop : -1.66 (0.30), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  38 
 TYR   0.015   0.001   TYR L  49 
 PHE   0.012   0.001   PHE A  20 
 TRP   0.008   0.001   TRP B 106 
 HIS   0.003   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7690)
  covalent geometry    : angle       0.50979 (10474)
  SS BOND              : bond        0.00367 (    5)
  SS BOND              : angle       0.71237 (   10)
  hydrogen bonds       : bond        0.11819 (  370)
  hydrogen bonds       : angle       5.52280 ( 1076)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  121 is missing expected H atoms. Skipping.
Residue LEU  293 is missing expected H atoms. Skipping.
Residue TYR  355 is missing expected H atoms. Skipping.
Residue TYR  369 is missing expected H atoms. Skipping.
Residue TYR  396 is missing expected H atoms. Skipping.
Residue MET  410 is missing expected H atoms. Skipping.
Evaluate side-chains
  156 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 141
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.8155 (tpt) cc_final: 0.7785 (tpt)
REVERT: A  348 MET cc_start: 0.5442 (ttt) cc_final: 0.5209 (tpt)
REVERT: A  423 MET cc_start: 0.7815 (ttt) cc_final: 0.7563 (ttm)
REVERT: B    4 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8239 (mp)
REVERT: B   25 SER cc_start: 0.8167 (p) cc_final: 0.7942 (m)
REVERT: B   34 MET cc_start: 0.7314 (mpp) cc_final: 0.6963 (mtt)
REVERT: L  170 ASP cc_start: 0.8551 (m-30) cc_final: 0.7814 (p0)
  outliers start: 15
  outliers final: 5
  residues processed: 151
  average time/residue: 0.2046
  time to fit residues: 41.5331
Evaluate side-chains
  114 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  266 ASP
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   31 ASP
Chi-restraints excluded: chain H residue   50 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.136189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.113236 restraints weight = 50956.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 3.06
r_work: 0.3598 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3606
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3606 r_free = 0.3606    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3606 r_free = 0.3606    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3606
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7695  Z= 0.135
  Angle     :  0.538   5.227  10484  Z= 0.288
  Chirality :  0.040   0.159   1199
  Planarity :  0.003   0.051   1303
  Dihedral  :  5.222  56.915   1069
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 12.45 %
    Favored  : 86.31 %
  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 aren not related in a simple way.
  whole:  0.37 (0.28), residues: 967
  helix:  2.06 (0.28), residues: 341
  sheet:  0.71 (0.36), residues: 224
  loop : -1.72 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  70 
 TYR   0.022   0.001   TYR A 257 
 PHE   0.025   0.001   PHE A  20 
 TRP   0.007   0.001   TRP H  47 
 HIS   0.005   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7690)
  covalent geometry    : angle       0.53721 (10474)
  SS BOND              : bond        0.01047 (    5)
  SS BOND              : angle       1.21178 (   10)
  hydrogen bonds       : bond        0.05236 (  370)
  hydrogen bonds       : angle       4.83890 ( 1076)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  121 is missing expected H atoms. Skipping.
Residue LEU  293 is missing expected H atoms. Skipping.
Residue TYR  355 is missing expected H atoms. Skipping.
Residue TYR  369 is missing expected H atoms. Skipping.
Residue TYR  396 is missing expected H atoms. Skipping.
Residue MET  410 is missing expected H atoms. Skipping.
Evaluate side-chains
  126 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.8240 (tpt) cc_final: 0.7892 (tpt)
REVERT: A  348 MET cc_start: 0.5421 (ttt) cc_final: 0.5166 (tpt)
REVERT: A  423 MET cc_start: 0.7929 (ttt) cc_final: 0.7660 (ttm)
REVERT: B    4 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8230 (mp)
REVERT: B   34 MET cc_start: 0.7331 (mpp) cc_final: 0.6997 (mtt)
REVERT: H   79 TYR cc_start: 0.8142 (m-80) cc_final: 0.7892 (m-80)
REVERT: L  170 ASP cc_start: 0.8645 (m-30) cc_final: 0.7831 (p0)
  outliers start: 10
  outliers final: 7
  residues processed: 123
  average time/residue: 0.1587
  time to fit residues: 27.5038
Evaluate side-chains
  115 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue  204 ASN
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue  163 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 88 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 90 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 78 optimal weight:    0.1980
   chunk 1 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    1.1184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.134957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.112509 restraints weight = 47456.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3686 rms_B_bonded: 2.91
r_work: 0.3590 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3597
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3597 r_free = 0.3597    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3597 r_free = 0.3597    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3597
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7695  Z= 0.147
  Angle     :  0.548   6.254  10484  Z= 0.292
  Chirality :  0.040   0.160   1199
  Planarity :  0.003   0.037   1303
  Dihedral  :  4.887  42.341   1065
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 13.19 %
    Favored  : 85.20 %
  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 aren not related in a simple way.
  whole:  0.25 (0.28), residues: 967
  helix:  1.97 (0.28), residues: 341
  sheet:  0.64 (0.36), residues: 224
  loop : -1.80 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  70 
 TYR   0.017   0.001   TYR L  49 
 PHE   0.021   0.001   PHE A  20 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.005   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 7690)
  covalent geometry    : angle       0.54811 (10474)
  SS BOND              : bond        0.00376 (    5)
  SS BOND              : angle       0.84766 (   10)
  hydrogen bonds       : bond        0.05014 (  370)
  hydrogen bonds       : angle       4.68909 ( 1076)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  121 is missing expected H atoms. Skipping.
Residue LEU  293 is missing expected H atoms. Skipping.
Residue TYR  355 is missing expected H atoms. Skipping.
Residue TYR  369 is missing expected H atoms. Skipping.
Residue TYR  396 is missing expected H atoms. Skipping.
Residue MET  410 is missing expected H atoms. Skipping.
Evaluate side-chains
  121 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.8307 (tpt) cc_final: 0.7922 (tpt)
REVERT: A  348 MET cc_start: 0.5408 (ttt) cc_final: 0.5134 (tpt)
REVERT: A  423 MET cc_start: 0.7938 (ttt) cc_final: 0.7665 (ttm)
REVERT: B    4 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8250 (mp)
REVERT: B   34 MET cc_start: 0.7333 (mpp) cc_final: 0.6987 (mtt)
REVERT: H  100 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8229 (mt)
REVERT: L  170 ASP cc_start: 0.8688 (m-30) cc_final: 0.7886 (p0)
  outliers start: 13
  outliers final: 6
  residues processed: 118
  average time/residue: 0.1480
  time to fit residues: 25.1236
Evaluate side-chains
  112 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue  100 LEU
Chi-restraints excluded: chain H residue  204 ASN
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue  163 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 54 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0870
   chunk 4 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 76 optimal weight:    0.6980
   overall best weight:    0.9562

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.135266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.112374 restraints weight = 52337.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 3.09
r_work: 0.3582 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3593
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3593 r_free = 0.3593    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3593 r_free = 0.3593    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3593
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.1903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7695  Z= 0.131
  Angle     :  0.530   4.897  10484  Z= 0.283
  Chirality :  0.040   0.156   1199
  Planarity :  0.003   0.031   1303
  Dihedral  :  4.850  41.967   1065
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 13.56 %
    Favored  : 84.71 %
  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 aren not related in a simple way.
  whole:  0.32 (0.28), residues: 967
  helix:  2.00 (0.28), residues: 341
  sheet:  0.66 (0.36), residues: 226
  loop : -1.74 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  70 
 TYR   0.028   0.001   TYR A 257 
 PHE   0.018   0.001   PHE A  20 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.005   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 7690)
  covalent geometry    : angle       0.53000 (10474)
  SS BOND              : bond        0.00377 (    5)
  SS BOND              : angle       0.67034 (   10)
  hydrogen bonds       : bond        0.04719 (  370)
  hydrogen bonds       : angle       4.54965 ( 1076)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  121 is missing expected H atoms. Skipping.
Residue LEU  293 is missing expected H atoms. Skipping.
Residue TYR  355 is missing expected H atoms. Skipping.
Residue TYR  369 is missing expected H atoms. Skipping.
Residue TYR  396 is missing expected H atoms. Skipping.
Residue MET  410 is missing expected H atoms. Skipping.
Evaluate side-chains
  125 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.8350 (tpt) cc_final: 0.7973 (tpt)
REVERT: A  239 MET cc_start: 0.8344 (mtp) cc_final: 0.7985 (mtp)
REVERT: A  423 MET cc_start: 0.7945 (ttt) cc_final: 0.7666 (ttm)
REVERT: B    4 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8250 (mp)
REVERT: B   34 MET cc_start: 0.7333 (mpp) cc_final: 0.6978 (mtt)
REVERT: H  100 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8218 (mt)
REVERT: L  170 ASP cc_start: 0.8736 (m-30) cc_final: 0.7843 (p0)
  outliers start: 14
  outliers final: 7
  residues processed: 122
  average time/residue: 0.1708
  time to fit residues: 29.2085
Evaluate side-chains
  114 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ASP
Chi-restraints excluded: chain A residue  266 ASP
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  431 ARG
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue  100 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue  163 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 83 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    1.9588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.132270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.109501 restraints weight = 50349.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 2.97
r_work: 0.3537 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3543
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3543 r_free = 0.3543    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3543 r_free = 0.3543    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3543
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   7695  Z= 0.219
  Angle     :  0.603   4.949  10484  Z= 0.328
  Chirality :  0.042   0.158   1199
  Planarity :  0.004   0.031   1303
  Dihedral  :  5.057  40.959   1063
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 14.18 %
    Favored  : 84.34 %
  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 aren not related in a simple way.
  whole: -0.01 (0.27), residues: 967
  helix:  1.60 (0.28), residues: 341
  sheet:  0.66 (0.35), residues: 230
  loop : -1.94 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  30 
 TYR   0.023   0.002   TYR L  49 
 PHE   0.012   0.002   PHE H 146 
 TRP   0.010   0.002   TRP B 106 
 HIS   0.004   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 7690)
  covalent geometry    : angle       0.60220 (10474)
  SS BOND              : bond        0.00454 (    5)
  SS BOND              : angle       0.99800 (   10)
  hydrogen bonds       : bond        0.05632 (  370)
  hydrogen bonds       : angle       4.85912 ( 1076)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  121 is missing expected H atoms. Skipping.
Residue LEU  293 is missing expected H atoms. Skipping.
Residue TYR  355 is missing expected H atoms. Skipping.
Residue TYR  369 is missing expected H atoms. Skipping.
Residue TYR  396 is missing expected H atoms. Skipping.
Residue MET  410 is missing expected H atoms. Skipping.
Evaluate side-chains
  115 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.8321 (tpt) cc_final: 0.7880 (tpt)
REVERT: A  227 ILE cc_start: 0.7257 (tt) cc_final: 0.6772 (pt)
REVERT: A  423 MET cc_start: 0.7936 (ttt) cc_final: 0.7659 (ttm)
REVERT: B    4 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8329 (mp)
REVERT: B   34 MET cc_start: 0.7439 (mpp) cc_final: 0.7127 (mtt)
REVERT: H  100 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8416 (mt)
REVERT: L  170 ASP cc_start: 0.8803 (m-30) cc_final: 0.8012 (p0)
  outliers start: 12
  outliers final: 8
  residues processed: 112
  average time/residue: 0.1545
  time to fit residues: 24.9319
Evaluate side-chains
  108 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ASP
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue  100 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue  163 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 62 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 17 optimal weight:    0.3980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B  83 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.135096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.112976 restraints weight = 44078.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 2.78
r_work: 0.3594 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3601
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3601 r_free = 0.3601    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3601 r_free = 0.3601    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3601
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.2206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7695  Z= 0.121
  Angle     :  0.535   4.827  10484  Z= 0.286
  Chirality :  0.040   0.158   1199
  Planarity :  0.003   0.029   1303
  Dihedral  :  4.855  40.948   1063
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 15.29 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.27 (0.27), residues: 967
  helix:  1.94 (0.28), residues: 335
  sheet:  0.92 (0.37), residues: 211
  loop : -1.78 (0.29), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 139 
 TYR   0.025   0.001   TYR A 257 
 PHE   0.013   0.001   PHE A  20 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.004   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 7690)
  covalent geometry    : angle       0.53502 (10474)
  SS BOND              : bond        0.00380 (    5)
  SS BOND              : angle       0.61717 (   10)
  hydrogen bonds       : bond        0.04781 (  370)
  hydrogen bonds       : angle       4.53853 ( 1076)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  121 is missing expected H atoms. Skipping.
Residue LEU  293 is missing expected H atoms. Skipping.
Residue TYR  355 is missing expected H atoms. Skipping.
Residue TYR  369 is missing expected H atoms. Skipping.
Residue TYR  396 is missing expected H atoms. Skipping.
Residue MET  410 is missing expected H atoms. Skipping.
Evaluate side-chains
  112 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.8337 (tpt) cc_final: 0.7949 (tpt)
REVERT: A  227 ILE cc_start: 0.7253 (tt) cc_final: 0.6983 (pt)
REVERT: A  423 MET cc_start: 0.7895 (ttt) cc_final: 0.7614 (ttm)
REVERT: B    4 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8291 (mp)
REVERT: B   34 MET cc_start: 0.7325 (mpp) cc_final: 0.6990 (mtt)
REVERT: H  100 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8244 (mt)
REVERT: L  170 ASP cc_start: 0.8748 (m-30) cc_final: 0.7922 (p0)
  outliers start: 10
  outliers final: 7
  residues processed: 111
  average time/residue: 0.1570
  time to fit residues: 25.2478
Evaluate side-chains
  111 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ASP
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue  100 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue  163 VAL
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 14 optimal weight:    0.4980
   chunk 8 optimal weight:    0.9980
   chunk 92 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
L 138 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.134628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.111719 restraints weight = 50626.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3673 rms_B_bonded: 3.01
r_work: 0.3574 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3578
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3578 r_free = 0.3578    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3578 r_free = 0.3578    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3578
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7695  Z= 0.140
  Angle     :  0.538   5.450  10484  Z= 0.289
  Chirality :  0.040   0.154   1199
  Planarity :  0.003   0.030   1303
  Dihedral  :  4.845  40.791   1063
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 15.41 %
    Favored  : 83.23 %
  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 aren not related in a simple way.
  whole:  0.31 (0.28), residues: 967
  helix:  1.92 (0.28), residues: 336
  sheet:  0.98 (0.36), residues: 215
  loop : -1.77 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  70 
 TYR   0.019   0.001   TYR L  49 
 PHE   0.012   0.001   PHE A  20 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.004   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 7690)
  covalent geometry    : angle       0.53795 (10474)
  SS BOND              : bond        0.00379 (    5)
  SS BOND              : angle       0.73534 (   10)
  hydrogen bonds       : bond        0.04780 (  370)
  hydrogen bonds       : angle       4.53168 ( 1076)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  121 is missing expected H atoms. Skipping.
Residue LEU  293 is missing expected H atoms. Skipping.
Residue TYR  355 is missing expected H atoms. Skipping.
Residue TYR  369 is missing expected H atoms. Skipping.
Residue TYR  396 is missing expected H atoms. Skipping.
Residue MET  410 is missing expected H atoms. Skipping.
Evaluate side-chains
  111 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.8360 (tpt) cc_final: 0.7972 (tpt)
REVERT: A  227 ILE cc_start: 0.7239 (tt) cc_final: 0.6877 (pt)
REVERT: A  423 MET cc_start: 0.7921 (ttt) cc_final: 0.7642 (ttm)
REVERT: B    4 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8312 (mp)
REVERT: B   34 MET cc_start: 0.7421 (mpp) cc_final: 0.7066 (mtt)
REVERT: H  100 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8265 (mt)
REVERT: L  170 ASP cc_start: 0.8754 (m-30) cc_final: 0.7943 (p0)
  outliers start: 11
  outliers final: 9
  residues processed: 109
  average time/residue: 0.1455
  time to fit residues: 23.1392
Evaluate side-chains
  110 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ASP
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue  100 LEU
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue  163 VAL
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    0.3980
   chunk 59 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0980
   chunk 0 optimal weight:    5.9990
   chunk 72 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
L 138 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.134684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.111610 restraints weight = 49846.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 3.03
r_work: 0.3586 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3594
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3594 r_free = 0.3594    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3594 r_free = 0.3594    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3594
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7695  Z= 0.124
  Angle     :  0.532   6.062  10484  Z= 0.283
  Chirality :  0.040   0.155   1199
  Planarity :  0.003   0.030   1303
  Dihedral  :  4.792  40.804   1063
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 15.29 %
    Favored  : 83.23 %
  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 aren not related in a simple way.
  whole:  0.36 (0.28), residues: 967
  helix:  1.98 (0.28), residues: 336
  sheet:  0.93 (0.36), residues: 217
  loop : -1.73 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 139 
 TYR   0.027   0.001   TYR A 257 
 PHE   0.012   0.001   PHE A  20 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.004   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7690)
  covalent geometry    : angle       0.53174 (10474)
  SS BOND              : bond        0.00361 (    5)
  SS BOND              : angle       0.64304 (   10)
  hydrogen bonds       : bond        0.04538 (  370)
  hydrogen bonds       : angle       4.43493 ( 1076)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  121 is missing expected H atoms. Skipping.
Residue LEU  293 is missing expected H atoms. Skipping.
Residue TYR  355 is missing expected H atoms. Skipping.
Residue TYR  369 is missing expected H atoms. Skipping.
Residue TYR  396 is missing expected H atoms. Skipping.
Residue MET  410 is missing expected H atoms. Skipping.
Evaluate side-chains
  115 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 MET cc_start: 0.7949 (mmp) cc_final: 0.7694 (mmp)
REVERT: A   62 MET cc_start: 0.8348 (tpt) cc_final: 0.7972 (tpt)
REVERT: A  227 ILE cc_start: 0.7307 (tt) cc_final: 0.6978 (pt)
REVERT: B    4 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8254 (mp)
REVERT: B   34 MET cc_start: 0.7387 (mpp) cc_final: 0.7037 (mtt)
REVERT: H  100 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8221 (mt)
REVERT: L  170 ASP cc_start: 0.8762 (m-30) cc_final: 0.7908 (p0)
  outliers start: 12
  outliers final: 9
  residues processed: 113
  average time/residue: 0.1571
  time to fit residues: 25.0808
Evaluate side-chains
  111 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ASP
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue  100 LEU
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue  163 VAL
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 55 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 76 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0980
   chunk 1 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.136084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.113179 restraints weight = 48434.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3710 rms_B_bonded: 3.00
r_work: 0.3611 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3615
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3615 r_free = 0.3615    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3615 r_free = 0.3615    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3615
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7695  Z= 0.106
  Angle     :  0.513   6.087  10484  Z= 0.272
  Chirality :  0.040   0.147   1199
  Planarity :  0.003   0.029   1303
  Dihedral  :  4.626  41.052   1063
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 15.41 %
    Favored  : 83.23 %
  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 aren not related in a simple way.
  whole:  0.47 (0.28), residues: 967
  helix:  2.05 (0.28), residues: 343
  sheet:  0.99 (0.36), residues: 215
  loop : -1.69 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  66 
 TYR   0.015   0.001   TYR L  49 
 PHE   0.012   0.001   PHE A  20 
 TRP   0.007   0.001   TRP H  47 
 HIS   0.003   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 7690)
  covalent geometry    : angle       0.51293 (10474)
  SS BOND              : bond        0.00336 (    5)
  SS BOND              : angle       0.51759 (   10)
  hydrogen bonds       : bond        0.04025 (  370)
  hydrogen bonds       : angle       4.25134 ( 1076)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  121 is missing expected H atoms. Skipping.
Residue LEU  293 is missing expected H atoms. Skipping.
Residue TYR  355 is missing expected H atoms. Skipping.
Residue TYR  369 is missing expected H atoms. Skipping.
Residue TYR  396 is missing expected H atoms. Skipping.
Residue MET  410 is missing expected H atoms. Skipping.
Evaluate side-chains
  114 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.8344 (tpt) cc_final: 0.8083 (tpt)
REVERT: A  227 ILE cc_start: 0.7332 (tt) cc_final: 0.7012 (pt)
REVERT: B    4 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8182 (mp)
REVERT: B   34 MET cc_start: 0.7353 (mpp) cc_final: 0.7023 (mtt)
REVERT: B   75 LYS cc_start: 0.9041 (mmpt) cc_final: 0.8706 (mmtt)
REVERT: H  100 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8173 (mt)
REVERT: L  170 ASP cc_start: 0.8746 (m-30) cc_final: 0.7904 (p0)
  outliers start: 11
  outliers final: 8
  residues processed: 112
  average time/residue: 0.1479
  time to fit residues: 23.9089
Evaluate side-chains
  111 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue  100 LEU
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue  163 VAL
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0370
   chunk 41 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   overall best weight:    0.9060

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.135946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.113920 restraints weight = 44062.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 2.78
r_work: 0.3613 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3622
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3622 r_free = 0.3622    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3622 r_free = 0.3622    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3622
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.2460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7695  Z= 0.125
  Angle     :  0.523   5.842  10484  Z= 0.278
  Chirality :  0.040   0.148   1199
  Planarity :  0.003   0.030   1303
  Dihedral  :  4.655  40.904   1063
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 15.41 %
    Favored  : 83.11 %
  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 aren not related in a simple way.
  whole:  0.44 (0.28), residues: 967
  helix:  2.03 (0.28), residues: 343
  sheet:  0.94 (0.37), residues: 216
  loop : -1.70 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  70 
 TYR   0.024   0.001   TYR A 257 
 PHE   0.011   0.001   PHE A  20 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.004   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 7690)
  covalent geometry    : angle       0.52310 (10474)
  SS BOND              : bond        0.00363 (    5)
  SS BOND              : angle       0.66414 (   10)
  hydrogen bonds       : bond        0.04268 (  370)
  hydrogen bonds       : angle       4.31464 ( 1076)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  121 is missing expected H atoms. Skipping.
Residue LEU  293 is missing expected H atoms. Skipping.
Residue TYR  355 is missing expected H atoms. Skipping.
Residue TYR  369 is missing expected H atoms. Skipping.
Residue TYR  396 is missing expected H atoms. Skipping.
Residue MET  410 is missing expected H atoms. Skipping.
Evaluate side-chains
  113 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 ILE cc_start: 0.7365 (tt) cc_final: 0.7060 (pt)
REVERT: B    4 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8200 (mp)
REVERT: B   34 MET cc_start: 0.7362 (mpp) cc_final: 0.7070 (mtt)
REVERT: B   75 LYS cc_start: 0.9054 (mmpt) cc_final: 0.8740 (mmtt)
REVERT: H  100 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8216 (mt)
REVERT: L  170 ASP cc_start: 0.8752 (m-30) cc_final: 0.7910 (p0)
  outliers start: 12
  outliers final: 10
  residues processed: 111
  average time/residue: 0.1433
  time to fit residues: 22.8891
Evaluate side-chains
  113 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ASP
Chi-restraints excluded: chain A residue   26 TYR
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  426 LEU
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue  100 LEU
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue  163 VAL
Chi-restraints excluded: chain L residue  196 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 91 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 16 optimal weight:    0.1980
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.135475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.113968 restraints weight = 53917.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3724 rms_B_bonded: 3.27
r_work: 0.3597 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3602
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3602 r_free = 0.3602    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3602 r_free = 0.3602    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3602
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.2511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7695  Z= 0.119
  Angle     :  0.521   5.903  10484  Z= 0.278
  Chirality :  0.040   0.152   1199
  Planarity :  0.003   0.030   1303
  Dihedral  :  4.645  40.955   1063
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 15.29 %
    Favored  : 83.11 %
  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 aren not related in a simple way.
  whole:  0.44 (0.28), residues: 967
  helix:  2.02 (0.28), residues: 343
  sheet:  0.94 (0.37), residues: 216
  loop : -1.68 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  70 
 TYR   0.029   0.001   TYR A 257 
 PHE   0.011   0.001   PHE A  20 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.004   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 7690)
  covalent geometry    : angle       0.52126 (10474)
  SS BOND              : bond        0.00347 (    5)
  SS BOND              : angle       0.62689 (   10)
  hydrogen bonds       : bond        0.04219 (  370)
  hydrogen bonds       : angle       4.28429 ( 1076)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3669.27 seconds
wall clock time: 62 minutes 54.71 seconds (3774.71 seconds total)