Starting phenix.real_space_refine
on Wed Mar 12 17:41:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jgf_36232/03_2025/8jgf_36232_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jgf_36232/03_2025/8jgf_36232.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jgf_36232/03_2025/8jgf_36232.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jgf_36232/03_2025/8jgf_36232.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jgf_36232/03_2025/8jgf_36232_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jgf_36232/03_2025/8jgf_36232_neut.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.035
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    5323      2.51       5
     N    1412      2.21       5
     O    1551      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8338
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1839
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1839
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 82
          Unresolved non-hydrogen dihedrals: 62
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 42
    Chain: "B"
      Number of atoms: 2477
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2477
          Classifications: {'peptide': 336}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 110
          Unresolved non-hydrogen angles: 137
          Unresolved non-hydrogen dihedrals: 93
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 2, 'ARG:plan': 8, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 81
    Chain: "E"
      Number of atoms: 1742
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1742
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 21
    Chain: "G"
      Number of atoms: 384
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 384
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "L"
      Number of atoms: 110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 110
          Classifications: {'peptide': 12}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 10}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "R"
      Number of atoms: 1786
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1786
          Classifications: {'peptide': 236}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 103
          Unresolved non-hydrogen angles: 123
          Unresolved non-hydrogen dihedrals: 85
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 49
  Time building chain proxies: 4.95, per 1000 atoms: 0.59
  Number of scatterers: 8338
  At special positions: 0
  Unit cell: (94.64, 119.6, 112.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      52     16.00
     O    1551      8.00
     N    1412      7.00
     C    5323      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  21 " - pdb=" SG  CYS E  95 " 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: 2.12
  Conformation dependent library (CDL) restraints added in 943.9 milliseconds
  

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2064

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 13 sheets defined
      37.9% alpha, 24.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.823A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 210 through 216
      removed outlier: 3.874A  pdb=" N   ASN A 216 " --> pdb=" O   GLN A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 245
    Processing helix  chain 'A' and resid 246 through 250
      removed outlier: 3.939A  pdb=" N   ARG A 250 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 271
    Processing helix  chain 'A' and resid 274 through 278
    Processing helix  chain 'A' and resid 279 through 285
    Processing helix  chain 'A' and resid 298 through 319
      removed outlier: 3.781A  pdb=" N   ILE A 315 " --> pdb=" O   GLU A 311 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   SER A 319 " --> pdb=" O   ILE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 358
    Processing helix  chain 'B' and resid 11 through 31
    Processing helix  chain 'B' and resid 34 through 40
    Processing helix  chain 'E' and resid 27 through 31
    Processing helix  chain 'E' and resid 86 through 90
    Processing helix  chain 'E' and resid 220 through 224
    Processing helix  chain 'G' and resid 10 through 23
    Processing helix  chain 'G' and resid 28 through 44
    Processing helix  chain 'R' and resid 26 through 28
      No H-bonds generated for 'chain 'R' and resid 26 through 28'
    Processing helix  chain 'R' and resid 29 through 55
      removed outlier: 3.796A  pdb=" N   CYS R  35 " --> pdb=" O   THR R  31 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 60 through 85
      removed outlier: 3.962A  pdb=" N   ASN R  67 " --> pdb=" O   ILE R  63 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 97 through 126
    Processing helix  chain 'R' and resid 126 through 133
    Processing helix  chain 'R' and resid 137 through 160
    Processing helix  chain 'R' and resid 175 through 205
    Processing helix  chain 'R' and resid 211 through 228
    Processing helix  chain 'R' and resid 229 through 239
      removed outlier: 4.459A  pdb=" N   GLY R 233 " --> pdb=" O   GLY R 229 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 245 through 252
    Processing helix  chain 'R' and resid 254 through 273
      Proline residue:  R 269  - end of helix
    Processing helix  chain 'R' and resid 273 through 278
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 9.092A  pdb=" N   ALA A 220 " --> pdb=" O   THR A  33 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   ILE A 222 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.268A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 8.557A  pdb=" N   ASP A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56
      removed outlier: 5.482A  pdb=" N   THR B  52 " --> pdb=" O   ASN B 345 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ASN B 345 " --> pdb=" O   THR B  52 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68
      removed outlier: 3.534A  pdb=" N   ALA B  65 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   SER B  79 " --> pdb=" O   LYS B  83 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LYS B  83 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   LEU B  84 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   ALA B  97 " --> pdb=" O   LEU B  84 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ILE B  86 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110
      removed outlier: 4.004A  pdb=" N   GLY B 121 " --> pdb=" O   ILE B 125 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   ILE B 125 " --> pdb=" O   GLY B 121 " (cutoff:3.500A)
      removed outlier: 5.832A  pdb=" N   CYS B 126 " --> pdb=" O   GLU B 143 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   GLU B 143 " --> pdb=" O   CYS B 126 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ILE B 128 " --> pdb=" O   SER B 141 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ARG B 139 " --> pdb=" O   ASN B 130 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 158
      removed outlier: 6.074A  pdb=" N   GLN B 161 " --> pdb=" O   LEU B 157 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   ASP B 175 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
      removed outlier: 5.906A  pdb=" N   GLN B 181 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197
      removed outlier: 3.653A  pdb=" N   GLN B 225 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ASP B 217 " --> pdb=" O   CYS B 223 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   CYS B 223 " --> pdb=" O   ASP B 217 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239
      removed outlier: 6.527A  pdb=" N   CYS B 255 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   THR B 268 " --> pdb=" O   CYS B 255 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   LEU B 257 " --> pdb=" O   LEU B 266 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283
      removed outlier: 3.635A  pdb=" N   SER B 280 " --> pdb=" O   GLY B 293 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   ASP B 303 " --> pdb=" O   ARG B 309 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   ARG B 309 " --> pdb=" O   ASP B 303 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6
    Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11
      removed outlier: 5.888A  pdb=" N   GLY E   9 " --> pdb=" O   THR E 117 " (cutoff:3.500A)
      removed outlier: 5.687A  pdb=" N   ARG E  37 " --> pdb=" O   TRP E  46 " (cutoff:3.500A)
      removed outlier: 5.096A  pdb=" N   TRP E  46 " --> pdb=" O   ARG E  37 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11
      removed outlier: 5.888A  pdb=" N   GLY E   9 " --> pdb=" O   THR E 117 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   PHE E 109 " --> pdb=" O   ARG E  97 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 3.951A  pdb=" N   GLU E 246 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)

    462 hydrogen bonds defined for protein.
    1275 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.50

  Time building geometry restraints manager: 2.51 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1409
        1.31 -     1.44: 2371
        1.44 -     1.56: 4663
        1.56 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 8515
  Sorted by residual:
  bond pdb=" CA  PHE B 240 "
       pdb=" C   PHE B 240 "
    ideal  model  delta    sigma   weight residual
    1.523  1.430  0.092 1.28e-02 6.10e+03 5.22e+01
  bond pdb=" CA  LYS L  19 "
       pdb=" C   LYS L  19 "
    ideal  model  delta    sigma   weight residual
    1.524  1.427  0.096 1.35e-02 5.49e+03 5.09e+01
  bond pdb=" CA  SER R 176 "
       pdb=" C   SER R 176 "
    ideal  model  delta    sigma   weight residual
    1.524  1.440  0.083 1.32e-02 5.74e+03 3.99e+01
  bond pdb=" CA  TRP R  50 "
       pdb=" C   TRP R  50 "
    ideal  model  delta    sigma   weight residual
    1.524  1.454  0.071 1.24e-02 6.50e+03 3.24e+01
  bond pdb=" CA  VAL R  48 "
       pdb=" C   VAL R  48 "
    ideal  model  delta    sigma   weight residual
    1.524  1.451  0.072 1.30e-02 5.92e+03 3.10e+01
  ... (remaining 8510 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.67: 11379
        2.67 -     5.34: 173
        5.34 -     8.01: 22
        8.01 -    10.68: 14
       10.68 -    13.35: 3
  Bond angle restraints: 11591
  Sorted by residual:
  angle pdb=" N   TYR R  64 "
        pdb=" CA  TYR R  64 "
        pdb=" C   TYR R  64 "
      ideal   model   delta    sigma   weight residual
     114.04  100.69   13.35 1.24e+00 6.50e-01 1.16e+02
  angle pdb=" N   ILE R  63 "
        pdb=" CA  ILE R  63 "
        pdb=" C   ILE R  63 "
      ideal   model   delta    sigma   weight residual
     112.83  102.73   10.10 9.90e-01 1.02e+00 1.04e+02
  angle pdb=" C   GLY A  45 "
        pdb=" N   LYS A  46 "
        pdb=" CA  LYS A  46 "
      ideal   model   delta    sigma   weight residual
     120.38  132.21  -11.83 1.37e+00 5.33e-01 7.46e+01
  angle pdb=" N   LEU B 157 "
        pdb=" CA  LEU B 157 "
        pdb=" C   LEU B 157 "
      ideal   model   delta    sigma   weight residual
     113.97  103.28   10.69 1.28e+00 6.10e-01 6.97e+01
  angle pdb=" N   THR R 175 "
        pdb=" CA  THR R 175 "
        pdb=" C   THR R 175 "
      ideal   model   delta    sigma   weight residual
     113.30  102.75   10.55 1.34e+00 5.57e-01 6.20e+01
  ... (remaining 11586 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 4438
       17.84 -    35.68: 420
       35.68 -    53.52: 97
       53.52 -    71.36: 20
       71.36 -    89.21: 11
  Dihedral angle restraints: 4986
    sinusoidal: 1794
      harmonic: 3192
  Sorted by residual:
  dihedral pdb=" C   MET L  15 "
           pdb=" N   MET L  15 "
           pdb=" CA  MET L  15 "
           pdb=" CB  MET L  15 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -108.45  -14.15     0      2.50e+00 1.60e-01 3.21e+01
  dihedral pdb=" CA  PHE E  31 "
           pdb=" C   PHE E  31 "
           pdb=" N   GLY E  32 "
           pdb=" CA  GLY E  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.45   20.55     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" C   PHE B 240 "
           pdb=" N   PHE B 240 "
           pdb=" CA  PHE B 240 "
           pdb=" CB  PHE B 240 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.58  -10.02     0      2.50e+00 1.60e-01 1.61e+01
  ... (remaining 4983 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1076
       0.052 -    0.104: 208
       0.104 -    0.156: 51
       0.156 -    0.207: 6
       0.207 -    0.259: 5
  Chirality restraints: 1346
  Sorted by residual:
  chirality pdb=" CA  ARG E 191 "
            pdb=" N   ARG E 191 "
            pdb=" C   ARG E 191 "
            pdb=" CB  ARG E 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CA  LYS B  83 "
            pdb=" N   LYS B  83 "
            pdb=" C   LYS B  83 "
            pdb=" CB  LYS B  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CA  MET L  15 "
            pdb=" N   MET L  15 "
            pdb=" C   MET L  15 "
            pdb=" CB  MET L  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.30e+00
  ... (remaining 1343 not shown)

  Planarity restraints: 1468
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU R 157 "   -0.018 2.00e-02 2.50e+03   3.54e-02 1.26e+01
        pdb=" C   GLU R 157 "    0.061 2.00e-02 2.50e+03
        pdb=" O   GLU R 157 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   TRP R 158 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 240 "    0.055 5.00e-02 4.00e+02   8.14e-02 1.06e+01
        pdb=" N   PRO B 241 "   -0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO B 241 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B 241 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN R  45 "    0.015 2.00e-02 2.50e+03   3.06e-02 9.37e+00
        pdb=" C   ASN R  45 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   ASN R  45 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ALA R  46 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1465 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1497
        2.76 -     3.29: 8373
        3.29 -     3.83: 14942
        3.83 -     4.36: 18121
        4.36 -     4.90: 30263
  Nonbonded interactions: 73196
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  63 "
            pdb=" OG  SER B 321 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OG  SER B 152 "
            pdb=" O   VAL B 192 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OE2 GLU B 265 "
            pdb=" OG1 THR B 268 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   THR B  91 "
            pdb=" OG1 THR B  92 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   HIS B  59 "
            pdb=" OG  SER B 339 "
     model   vdw
     2.285 3.040
  ... (remaining 73191 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     22.000
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
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      :  0.008   0.096   8515  Z= 0.502
  Angle     :  0.860  13.354  11591  Z= 0.565
  Chirality :  0.047   0.259   1346
  Planarity :  0.005   0.081   1468
  Dihedral  : 15.546  89.206   2919
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 20.21 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.26), residues: 1081
  helix:  1.25 (0.28), residues: 362
  sheet: -0.50 (0.29), residues: 281
  loop : -0.22 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R 158 
 HIS   0.007   0.001   HIS B 147 
 PHE   0.024   0.002   PHE B 240 
 TYR   0.028   0.002   TYR R  64 
 ARG   0.004   0.001   ARG E 191 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 287
  time to evaluate  : 3.388 
Fit side-chains
REVERT: A   49 ILE cc_start: 0.7450 (mt) cc_final: 0.7078 (OUTLIER)
REVERT: B   25 ASP cc_start: 0.6993 (m-30) cc_final: 0.6791 (m-30)
REVERT: B  258 PHE cc_start: 0.8034 (m-80) cc_final: 0.7740 (m-80)
REVERT: B  263 ASP cc_start: 0.7212 (t70) cc_final: 0.6962 (t0)
REVERT: R   80 LEU cc_start: 0.7865 (tp) cc_final: 0.7507 (tt)
  outliers start: 5
  outliers final: 2
  residues processed: 289
  average time/residue: 1.1522
  time to fit residues: 354.4025
Evaluate side-chains
  227 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 226
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  234 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9990
   chunk 45 optimal weight:    0.3980
   chunk 27 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 84 optimal weight:    0.4980
   chunk 32 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 259 ASN
B  37 GLN
B 137 ASN
B 180 GLN
B 264 GLN
E  76 ASN
E 171 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.115716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.106332 restraints weight = 12744.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 1.85
r_work: 0.3450 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8515  Z= 0.213
  Angle     :  0.566   7.247  11591  Z= 0.302
  Chirality :  0.042   0.155   1346
  Planarity :  0.005   0.056   1468
  Dihedral  :  4.399  21.011   1179
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 23.34 %
    Favored  : 71.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.26), residues: 1081
  helix:  1.99 (0.27), residues: 370
  sheet: -0.20 (0.30), residues: 273
  loop :  0.06 (0.32), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 174 
 HIS   0.003   0.001   HIS R 133 
 PHE   0.022   0.002   PHE E  28 
 TYR   0.028   0.002   TYR L  17 
 ARG   0.011   0.001   ARG B 256 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 266
  time to evaluate  : 0.946 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8567 (mptm) cc_final: 0.8356 (mptm)
REVERT: A   43 ASN cc_start: 0.8573 (p0) cc_final: 0.8370 (p0)
REVERT: A   53 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7656 (mtm)
REVERT: A  186 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6943 (tm-30)
REVERT: A  192 ASP cc_start: 0.7488 (m-30) cc_final: 0.7172 (m-30)
REVERT: A  267 LYS cc_start: 0.8781 (ttmm) cc_final: 0.8501 (ttmt)
REVERT: A  314 ASP cc_start: 0.8021 (m-30) cc_final: 0.7552 (m-30)
REVERT: A  336 THR cc_start: 0.8296 (p) cc_final: 0.8047 (p)
REVERT: B   18 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7798 (tm-30)
REVERT: B   19 LEU cc_start: 0.8799 (mm) cc_final: 0.8193 (mm)
REVERT: B   35 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7997 (tp)
REVERT: B   37 GLN cc_start: 0.8273 (mt0) cc_final: 0.8026 (mt0)
REVERT: B  142 ARG cc_start: 0.8308 (ttm110) cc_final: 0.7729 (ttp-170)
REVERT: B  177 GLU cc_start: 0.8226 (tp30) cc_final: 0.7929 (tp30)
REVERT: B  191 ASP cc_start: 0.7964 (m-30) cc_final: 0.7701 (m-30)
REVERT: B  258 PHE cc_start: 0.8815 (m-80) cc_final: 0.8540 (m-80)
REVERT: B  263 ASP cc_start: 0.8145 (t70) cc_final: 0.7541 (t0)
REVERT: E   16 SER cc_start: 0.8675 (p) cc_final: 0.8338 (t)
REVERT: E  118 VAL cc_start: 0.8631 (t) cc_final: 0.8375 (m)
REVERT: E  213 THR cc_start: 0.8547 (t) cc_final: 0.8223 (p)
REVERT: R   36 ILE cc_start: 0.8481 (mp) cc_final: 0.8279 (mp)
REVERT: R   47 VAL cc_start: 0.8737 (t) cc_final: 0.8473 (p)
REVERT: R   98 LEU cc_start: 0.8185 (mm) cc_final: 0.7954 (tp)
REVERT: R  101 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8309 (p)
REVERT: R  152 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8483 (tp)
REVERT: R  203 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8183 (mm)
  outliers start: 42
  outliers final: 13
  residues processed: 287
  average time/residue: 0.9589
  time to fit residues: 297.4488
Evaluate side-chains
  278 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 260
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  319 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  152 LEU
Chi-restraints excluded: chain R residue  196 LEU
Chi-restraints excluded: chain R residue  203 LEU
Chi-restraints excluded: chain R residue  258 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 84 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 101 optimal weight:   10.0000
   chunk 89 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 259 ASN
A 338 ASN
A 354 ASN
B  21 ASN
B 225 GLN
B 264 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.114948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.105587 restraints weight = 13001.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 1.86
r_work: 0.3437 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3312 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.3010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8515  Z= 0.210
  Angle     :  0.533   8.315  11591  Z= 0.280
  Chirality :  0.042   0.180   1346
  Planarity :  0.004   0.061   1468
  Dihedral  :  4.137  20.145   1177
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 26.25 %
    Favored  : 69.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.26), residues: 1081
  helix:  2.52 (0.26), residues: 366
  sheet: -0.09 (0.30), residues: 277
  loop :  0.15 (0.32), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 211 
 HIS   0.009   0.001   HIS A 329 
 PHE   0.028   0.002   PHE E  28 
 TYR   0.033   0.001   TYR L  17 
 ARG   0.009   0.001   ARG B  54 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 263
  time to evaluate  : 0.855 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.8798 (p0) cc_final: 0.8424 (p0)
REVERT: A  186 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6922 (tm-30)
REVERT: A  205 ARG cc_start: 0.8728 (mtp-110) cc_final: 0.8405 (mtp-110)
REVERT: A  297 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6818 (mm-30)
REVERT: A  314 ASP cc_start: 0.8070 (m-30) cc_final: 0.7587 (m-30)
REVERT: A  329 HIS cc_start: 0.8511 (m-70) cc_final: 0.8305 (m170)
REVERT: A  331 THR cc_start: 0.8249 (p) cc_final: 0.8019 (t)
REVERT: A  337 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7628 (mp0)
REVERT: A  340 ARG cc_start: 0.8594 (tpp-160) cc_final: 0.8287 (tpt170)
REVERT: B   18 GLN cc_start: 0.8348 (tm-30) cc_final: 0.7884 (tm-30)
REVERT: B   19 LEU cc_start: 0.8854 (mm) cc_final: 0.8285 (mm)
REVERT: B   37 GLN cc_start: 0.8317 (mt0) cc_final: 0.8084 (mt0)
REVERT: B  191 ASP cc_start: 0.7947 (m-30) cc_final: 0.7644 (m-30)
REVERT: B  258 PHE cc_start: 0.8821 (m-80) cc_final: 0.8146 (m-80)
REVERT: B  263 ASP cc_start: 0.8106 (t70) cc_final: 0.7609 (t0)
REVERT: E   16 SER cc_start: 0.8558 (p) cc_final: 0.8258 (t)
REVERT: E   42 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8396 (mppt)
REVERT: E  118 VAL cc_start: 0.8614 (t) cc_final: 0.8385 (m)
REVERT: E  203 PHE cc_start: 0.8542 (m-80) cc_final: 0.7865 (m-80)
REVERT: E  213 THR cc_start: 0.8479 (t) cc_final: 0.8179 (p)
REVERT: R   36 ILE cc_start: 0.8531 (mp) cc_final: 0.8269 (mp)
REVERT: R   47 VAL cc_start: 0.8636 (t) cc_final: 0.8392 (p)
REVERT: R  101 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8286 (p)
REVERT: R  152 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8466 (tp)
REVERT: R  203 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8165 (mm)
REVERT: R  218 ILE cc_start: 0.8476 (mt) cc_final: 0.8239 (tt)
  outliers start: 35
  outliers final: 16
  residues processed: 278
  average time/residue: 1.1596
  time to fit residues: 346.8772
Evaluate side-chains
  282 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 261
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain B residue   45 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain E residue   42 LYS
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain E residue  237 LEU
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  152 LEU
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  180 THR
Chi-restraints excluded: chain R residue  203 LEU
Chi-restraints excluded: chain R residue  258 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 97 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 99 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 104 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 91 optimal weight:    0.1980
   chunk 33 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 259 ASN
A 338 ASN
B  11 GLN
B 225 GLN
E 194 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.115112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.105751 restraints weight = 12976.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 1.86
r_work: 0.3439 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.3380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8515  Z= 0.192
  Angle     :  0.520   8.061  11591  Z= 0.273
  Chirality :  0.041   0.166   1346
  Planarity :  0.004   0.060   1468
  Dihedral  :  4.026  19.782   1177
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 27.29 %
    Favored  : 67.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.26), residues: 1081
  helix:  2.65 (0.26), residues: 366
  sheet:  0.02 (0.30), residues: 271
  loop :  0.08 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 211 
 HIS   0.005   0.001   HIS A 329 
 PHE   0.028   0.002   PHE E  28 
 TYR   0.031   0.001   TYR L  17 
 ARG   0.009   0.001   ARG A 300 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 267
  time to evaluate  : 1.816 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.8886 (p0) cc_final: 0.8447 (p0)
REVERT: A  186 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6915 (tm-30)
REVERT: A  192 ASP cc_start: 0.7491 (m-30) cc_final: 0.7002 (m-30)
REVERT: A  205 ARG cc_start: 0.8709 (mtp-110) cc_final: 0.8374 (mtm-85)
REVERT: A  297 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6745 (mm-30)
REVERT: A  298 ASP cc_start: 0.7825 (t0) cc_final: 0.7598 (t0)
REVERT: A  314 ASP cc_start: 0.8059 (m-30) cc_final: 0.7667 (m-30)
REVERT: A  337 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7554 (mp0)
REVERT: A  340 ARG cc_start: 0.8583 (tpp-160) cc_final: 0.8113 (tpp-160)
REVERT: B   18 GLN cc_start: 0.8380 (tm-30) cc_final: 0.7912 (tm-30)
REVERT: B   19 LEU cc_start: 0.8865 (mm) cc_final: 0.8320 (mm)
REVERT: B   37 GLN cc_start: 0.8348 (mt0) cc_final: 0.8129 (mt0)
REVERT: B  191 ASP cc_start: 0.7938 (m-30) cc_final: 0.7593 (m-30)
REVERT: B  222 MET cc_start: 0.7855 (mmp) cc_final: 0.7563 (mmp)
REVERT: B  258 PHE cc_start: 0.8827 (m-80) cc_final: 0.8137 (m-80)
REVERT: B  263 ASP cc_start: 0.8066 (t70) cc_final: 0.7515 (t0)
REVERT: E   16 SER cc_start: 0.8531 (p) cc_final: 0.8237 (t)
REVERT: E   42 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8462 (mppt)
REVERT: E  203 PHE cc_start: 0.8537 (m-80) cc_final: 0.7854 (m-80)
REVERT: E  213 THR cc_start: 0.8467 (t) cc_final: 0.8183 (p)
REVERT: R   36 ILE cc_start: 0.8507 (mp) cc_final: 0.8253 (mp)
REVERT: R  101 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8274 (p)
REVERT: R  152 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8412 (tp)
REVERT: R  203 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8169 (mm)
REVERT: R  218 ILE cc_start: 0.8478 (mt) cc_final: 0.8208 (tt)
  outliers start: 42
  outliers final: 22
  residues processed: 285
  average time/residue: 1.2014
  time to fit residues: 370.7934
Evaluate side-chains
  275 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 248
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain E residue   42 LYS
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain E residue  237 LEU
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  152 LEU
Chi-restraints excluded: chain R residue  180 THR
Chi-restraints excluded: chain R residue  203 LEU
Chi-restraints excluded: chain R residue  258 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9990
   chunk 64 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 102 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 79 optimal weight:    4.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 259 ASN
B  11 GLN
B 225 GLN
B 264 GLN
E 142 GLN
E 194 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.115377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.105962 restraints weight = 12616.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 1.84
r_work: 0.3439 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.3569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8515  Z= 0.225
  Angle     :  0.537   8.124  11591  Z= 0.279
  Chirality :  0.042   0.163   1346
  Planarity :  0.004   0.060   1468
  Dihedral  :  4.064  19.340   1177
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 28.11 %
    Favored  : 67.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.26), residues: 1081
  helix:  2.73 (0.26), residues: 366
  sheet: -0.01 (0.31), residues: 273
  loop :  0.03 (0.31), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 211 
 HIS   0.004   0.001   HIS A 329 
 PHE   0.032   0.002   PHE E  28 
 TYR   0.032   0.001   TYR L  17 
 ARG   0.008   0.001   ARG A 300 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 257
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ASN cc_start: 0.8895 (p0) cc_final: 0.8519 (p0)
REVERT: A  186 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6939 (tm-30)
REVERT: A  192 ASP cc_start: 0.7533 (m-30) cc_final: 0.7020 (m-30)
REVERT: A  205 ARG cc_start: 0.8710 (mtp-110) cc_final: 0.8373 (mtm-85)
REVERT: A  208 ARG cc_start: 0.8212 (ptp90) cc_final: 0.7952 (ptp90)
REVERT: A  267 LYS cc_start: 0.8508 (ttmm) cc_final: 0.8235 (ptmt)
REVERT: A  297 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6820 (mm-30)
REVERT: A  298 ASP cc_start: 0.7859 (t0) cc_final: 0.7643 (t0)
REVERT: A  314 ASP cc_start: 0.8023 (m-30) cc_final: 0.7647 (m-30)
REVERT: A  337 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7516 (mp0)
REVERT: A  340 ARG cc_start: 0.8577 (tpp-160) cc_final: 0.8104 (tpp-160)
REVERT: B   18 GLN cc_start: 0.8407 (tm-30) cc_final: 0.7933 (tm-30)
REVERT: B   19 LEU cc_start: 0.8898 (mm) cc_final: 0.8340 (mm)
REVERT: B   37 GLN cc_start: 0.8348 (mt0) cc_final: 0.8111 (mt0)
REVERT: B   66 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7863 (ttp)
REVERT: B  191 ASP cc_start: 0.8002 (m-30) cc_final: 0.7637 (m-30)
REVERT: B  232 SER cc_start: 0.8492 (m) cc_final: 0.8127 (t)
REVERT: B  258 PHE cc_start: 0.8833 (m-80) cc_final: 0.8158 (m-80)
REVERT: B  263 ASP cc_start: 0.8082 (t70) cc_final: 0.7526 (t0)
REVERT: E   16 SER cc_start: 0.8515 (p) cc_final: 0.8217 (t)
REVERT: E   42 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8629 (mtpt)
REVERT: E  139 VAL cc_start: 0.8528 (t) cc_final: 0.8288 (p)
REVERT: E  203 PHE cc_start: 0.8556 (m-80) cc_final: 0.7845 (m-80)
REVERT: E  213 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8175 (p)
REVERT: E  237 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8081 (mt)
REVERT: R   36 ILE cc_start: 0.8525 (mp) cc_final: 0.8250 (mp)
REVERT: R   52 LEU cc_start: 0.8710 (mt) cc_final: 0.8487 (mm)
REVERT: R   84 LEU cc_start: 0.8346 (mt) cc_final: 0.8127 (mp)
REVERT: R  101 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8279 (p)
REVERT: R  125 LEU cc_start: 0.8850 (mp) cc_final: 0.8617 (mt)
REVERT: R  152 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8425 (tp)
REVERT: R  203 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8269 (mm)
  outliers start: 42
  outliers final: 21
  residues processed: 272
  average time/residue: 0.9631
  time to fit residues: 281.3811
Evaluate side-chains
  279 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 250
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  247 ARG
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain B residue   66 MET
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain E residue   42 LYS
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain E residue  213 THR
Chi-restraints excluded: chain E residue  237 LEU
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  102 MET
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  152 LEU
Chi-restraints excluded: chain R residue  180 THR
Chi-restraints excluded: chain R residue  203 LEU
Chi-restraints excluded: chain R residue  258 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 106 optimal weight:    0.9990
   chunk 9 optimal weight:    0.4980
   chunk 59 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0070
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.6602

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

Flipped N/Q/H residues before XYZ refinement:
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 259 ASN
A 338 ASN
B  11 GLN
B 225 GLN
E 194 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.117316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.108039 restraints weight = 12481.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 1.81
r_work: 0.3462 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3341 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.3762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8515  Z= 0.181
  Angle     :  0.525   7.834  11591  Z= 0.273
  Chirality :  0.041   0.157   1346
  Planarity :  0.004   0.059   1468
  Dihedral  :  4.009  18.645   1177
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 27.99 %
    Favored  : 67.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.26), residues: 1081
  helix:  2.82 (0.26), residues: 366
  sheet:  0.13 (0.32), residues: 272
  loop :  0.01 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 211 
 HIS   0.003   0.001   HIS A 329 
 PHE   0.033   0.002   PHE E  28 
 TYR   0.022   0.001   TYR L  17 
 ARG   0.008   0.001   ARG A 300 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 263
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 LYS cc_start: 0.8606 (ttmm) cc_final: 0.8393 (ttmm)
REVERT: A   43 ASN cc_start: 0.8883 (p0) cc_final: 0.8588 (p0)
REVERT: A  192 ASP cc_start: 0.7570 (m-30) cc_final: 0.7126 (m-30)
REVERT: A  205 ARG cc_start: 0.8699 (mtp-110) cc_final: 0.8398 (mtm-85)
REVERT: A  267 LYS cc_start: 0.8489 (ttmm) cc_final: 0.8198 (ptmt)
REVERT: A  297 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6922 (mm-30)
REVERT: A  314 ASP cc_start: 0.7987 (m-30) cc_final: 0.7613 (m-30)
REVERT: A  337 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7432 (mp0)
REVERT: B   18 GLN cc_start: 0.8398 (tm-30) cc_final: 0.7968 (tm-30)
REVERT: B   19 LEU cc_start: 0.8926 (mm) cc_final: 0.8374 (mm)
REVERT: B   37 GLN cc_start: 0.8357 (mt0) cc_final: 0.8144 (mt0)
REVERT: B   66 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7704 (ttp)
REVERT: B  191 ASP cc_start: 0.7981 (m-30) cc_final: 0.7644 (m-30)
REVERT: B  263 ASP cc_start: 0.7996 (t0) cc_final: 0.7416 (t0)
REVERT: B  291 LEU cc_start: 0.8515 (mp) cc_final: 0.8304 (mt)
REVERT: E   16 SER cc_start: 0.8380 (p) cc_final: 0.8121 (t)
REVERT: E   20 SER cc_start: 0.8169 (m) cc_final: 0.7853 (t)
REVERT: E   42 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8652 (mtpt)
REVERT: E   68 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8651 (p)
REVERT: E  139 VAL cc_start: 0.8466 (t) cc_final: 0.8222 (p)
REVERT: E  203 PHE cc_start: 0.8553 (m-80) cc_final: 0.7893 (m-80)
REVERT: E  206 SER cc_start: 0.8557 (t) cc_final: 0.8205 (p)
REVERT: E  213 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8068 (p)
REVERT: E  237 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8088 (mt)
REVERT: R   36 ILE cc_start: 0.8505 (mp) cc_final: 0.8268 (mp)
REVERT: R   52 LEU cc_start: 0.8584 (mt) cc_final: 0.8368 (mm)
REVERT: R   84 LEU cc_start: 0.8319 (mt) cc_final: 0.8100 (mp)
REVERT: R  101 VAL cc_start: 0.8589 (t) cc_final: 0.8330 (p)
REVERT: R  152 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8342 (tp)
  outliers start: 42
  outliers final: 22
  residues processed: 281
  average time/residue: 1.0549
  time to fit residues: 316.8152
Evaluate side-chains
  282 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 254
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain B residue   66 MET
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain E residue   42 LYS
Chi-restraints excluded: chain E residue   68 THR
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain E residue  213 THR
Chi-restraints excluded: chain E residue  237 LEU
Chi-restraints excluded: chain R residue  102 MET
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  152 LEU
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  180 THR
Chi-restraints excluded: chain R residue  219 LEU
Chi-restraints excluded: chain R residue  249 LEU
Chi-restraints excluded: chain R residue  258 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 28 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0980
   chunk 103 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 20 optimal weight:    5.9990
   chunk 95 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 79 optimal weight:    6.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 259 ASN
A 338 ASN
A 354 ASN
B 225 GLN
B 264 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.117115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.107848 restraints weight = 12511.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 1.82
r_work: 0.3464 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3342 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.3882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8515  Z= 0.196
  Angle     :  0.548   7.976  11591  Z= 0.282
  Chirality :  0.042   0.160   1346
  Planarity :  0.004   0.059   1468
  Dihedral  :  4.002  18.192   1177
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 29.15 %
    Favored  : 66.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.26), residues: 1081
  helix:  2.84 (0.25), residues: 369
  sheet:  0.07 (0.32), residues: 271
  loop : -0.09 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 211 
 HIS   0.003   0.001   HIS A 329 
 PHE   0.035   0.002   PHE E  28 
 TYR   0.016   0.001   TYR E 175 
 ARG   0.014   0.001   ARG A 247 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 262
  time to evaluate  : 1.035 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.8865 (p0) cc_final: 0.8617 (p0)
REVERT: A  192 ASP cc_start: 0.7530 (m-30) cc_final: 0.7082 (m-30)
REVERT: A  205 ARG cc_start: 0.8689 (mtp-110) cc_final: 0.8379 (mtm-85)
REVERT: A  297 GLU cc_start: 0.7380 (mm-30) cc_final: 0.6806 (mm-30)
REVERT: A  314 ASP cc_start: 0.7980 (m-30) cc_final: 0.7605 (m-30)
REVERT: A  337 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7398 (mp0)
REVERT: B   18 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7979 (tm-30)
REVERT: B   19 LEU cc_start: 0.8946 (mm) cc_final: 0.8369 (mm)
REVERT: B   37 GLN cc_start: 0.8375 (mt0) cc_final: 0.8166 (mt0)
REVERT: B   66 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7608 (ttp)
REVERT: B  191 ASP cc_start: 0.8004 (m-30) cc_final: 0.7641 (m-30)
REVERT: B  263 ASP cc_start: 0.8059 (t0) cc_final: 0.7537 (t0)
REVERT: B  291 LEU cc_start: 0.8512 (mp) cc_final: 0.8298 (mt)
REVERT: E   16 SER cc_start: 0.8363 (p) cc_final: 0.8109 (t)
REVERT: E   20 SER cc_start: 0.8232 (m) cc_final: 0.7897 (t)
REVERT: E   42 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8641 (mtpt)
REVERT: E   68 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8646 (p)
REVERT: E  139 VAL cc_start: 0.8451 (t) cc_final: 0.8172 (p)
REVERT: E  174 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8267 (tm)
REVERT: E  206 SER cc_start: 0.8522 (t) cc_final: 0.8199 (p)
REVERT: E  213 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8058 (p)
REVERT: E  237 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8200 (mt)
REVERT: R   36 ILE cc_start: 0.8521 (mp) cc_final: 0.8278 (mp)
REVERT: R   52 LEU cc_start: 0.8584 (mt) cc_final: 0.8383 (mm)
REVERT: R   84 LEU cc_start: 0.8319 (mt) cc_final: 0.8105 (mp)
REVERT: R  101 VAL cc_start: 0.8577 (t) cc_final: 0.8317 (p)
REVERT: R  152 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8318 (tp)
  outliers start: 34
  outliers final: 23
  residues processed: 278
  average time/residue: 1.0733
  time to fit residues: 319.2850
Evaluate side-chains
  284 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 254
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain B residue   66 MET
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain E residue   42 LYS
Chi-restraints excluded: chain E residue   68 THR
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  174 LEU
Chi-restraints excluded: chain E residue  213 THR
Chi-restraints excluded: chain E residue  237 LEU
Chi-restraints excluded: chain G residue   45 LYS
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  152 LEU
Chi-restraints excluded: chain R residue  180 THR
Chi-restraints excluded: chain R residue  200 ILE
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  249 LEU
Chi-restraints excluded: chain R residue  258 ILE
Chi-restraints excluded: chain R residue  275 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 46 optimal weight:    0.2980
   chunk 83 optimal weight:    3.9990
   chunk 56 optimal weight:    6.9990
   chunk 102 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 71 optimal weight:    4.9990
   chunk 52 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.8386

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

Flipped N/Q/H residues before XYZ refinement:
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 ASN
A 354 ASN
B  93 ASN
B 225 GLN
B 264 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.117013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.107754 restraints weight = 12597.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 1.81
r_work: 0.3462 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3340 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.3963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8515  Z= 0.213
  Angle     :  0.563   9.191  11591  Z= 0.289
  Chirality :  0.043   0.208   1346
  Planarity :  0.004   0.059   1468
  Dihedral  :  4.034  19.150   1177
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 30.31 %
    Favored  : 65.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.26), residues: 1081
  helix:  2.78 (0.25), residues: 370
  sheet:  0.08 (0.32), residues: 271
  loop : -0.14 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 211 
 HIS   0.004   0.001   HIS B 188 
 PHE   0.036   0.002   PHE E  28 
 TYR   0.020   0.001   TYR L  17 
 ARG   0.009   0.001   ARG A 247 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 259
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ASN cc_start: 0.8898 (p0) cc_final: 0.8611 (p0)
REVERT: A  192 ASP cc_start: 0.7519 (m-30) cc_final: 0.7188 (m-30)
REVERT: A  205 ARG cc_start: 0.8678 (mtp-110) cc_final: 0.8114 (mtm-85)
REVERT: A  267 LYS cc_start: 0.8351 (ttmm) cc_final: 0.8128 (ptpt)
REVERT: A  297 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6807 (mm-30)
REVERT: A  314 ASP cc_start: 0.7998 (m-30) cc_final: 0.7623 (m-30)
REVERT: B   11 GLN cc_start: 0.8234 (pp30) cc_final: 0.8022 (pp30)
REVERT: B   18 GLN cc_start: 0.8422 (tm-30) cc_final: 0.7980 (tm-30)
REVERT: B   19 LEU cc_start: 0.8974 (mm) cc_final: 0.8397 (mm)
REVERT: B   37 GLN cc_start: 0.8384 (mt0) cc_final: 0.8174 (mt0)
REVERT: B   93 ASN cc_start: 0.8056 (m-40) cc_final: 0.7840 (m110)
REVERT: B  191 ASP cc_start: 0.7963 (m-30) cc_final: 0.7345 (m-30)
REVERT: B  251 ASP cc_start: 0.8065 (m-30) cc_final: 0.7852 (m-30)
REVERT: B  263 ASP cc_start: 0.8077 (t0) cc_final: 0.7566 (t0)
REVERT: B  291 LEU cc_start: 0.8515 (mp) cc_final: 0.8305 (mt)
REVERT: E   16 SER cc_start: 0.8370 (p) cc_final: 0.8121 (t)
REVERT: E   20 SER cc_start: 0.8214 (m) cc_final: 0.7876 (t)
REVERT: E   42 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8635 (mtpt)
REVERT: E   68 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8646 (p)
REVERT: E  139 VAL cc_start: 0.8451 (t) cc_final: 0.8175 (p)
REVERT: E  174 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8258 (tm)
REVERT: E  206 SER cc_start: 0.8551 (t) cc_final: 0.8231 (p)
REVERT: E  213 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8056 (p)
REVERT: R   36 ILE cc_start: 0.8513 (mp) cc_final: 0.8268 (mp)
REVERT: R   52 LEU cc_start: 0.8551 (mt) cc_final: 0.8349 (mm)
REVERT: R   84 LEU cc_start: 0.8345 (mt) cc_final: 0.8130 (mp)
REVERT: R  101 VAL cc_start: 0.8585 (t) cc_final: 0.8331 (p)
REVERT: R  152 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8325 (tp)
  outliers start: 33
  outliers final: 22
  residues processed: 275
  average time/residue: 1.0969
  time to fit residues: 323.2508
Evaluate side-chains
  282 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 255
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  188 LYS
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain E residue   42 LYS
Chi-restraints excluded: chain E residue   68 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  174 LEU
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain E residue  213 THR
Chi-restraints excluded: chain G residue   45 LYS
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  152 LEU
Chi-restraints excluded: chain R residue  180 THR
Chi-restraints excluded: chain R residue  258 ILE
Chi-restraints excluded: chain R residue  275 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 94 optimal weight:    0.6980
   chunk 47 optimal weight:    4.9990
   chunk 21 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 101 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 ASN
B 225 GLN
B 264 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.116206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.106972 restraints weight = 12595.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 1.81
r_work: 0.3452 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.4009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8515  Z= 0.253
  Angle     :  0.587  10.763  11591  Z= 0.300
  Chirality :  0.044   0.325   1346
  Planarity :  0.004   0.045   1468
  Dihedral  :  4.106  19.431   1177
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 31.13 %
    Favored  : 65.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.26), residues: 1081
  helix:  2.70 (0.25), residues: 371
  sheet:  0.08 (0.32), residues: 277
  loop : -0.08 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 211 
 HIS   0.003   0.001   HIS A 329 
 PHE   0.038   0.002   PHE E  28 
 TYR   0.015   0.001   TYR E 190 
 ARG   0.009   0.001   ARG B  24 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 251
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 LYS cc_start: 0.8596 (ttmm) cc_final: 0.8368 (ttmm)
REVERT: A   43 ASN cc_start: 0.8928 (p0) cc_final: 0.8651 (p0)
REVERT: A  192 ASP cc_start: 0.7536 (m-30) cc_final: 0.7160 (m-30)
REVERT: A  198 MET cc_start: 0.8720 (mtm) cc_final: 0.8401 (ttp)
REVERT: A  205 ARG cc_start: 0.8701 (mtp-110) cc_final: 0.8338 (mtm-85)
REVERT: A  267 LYS cc_start: 0.8390 (ttmm) cc_final: 0.8116 (ptpt)
REVERT: A  297 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6834 (mm-30)
REVERT: A  314 ASP cc_start: 0.8050 (m-30) cc_final: 0.7668 (m-30)
REVERT: B   11 GLN cc_start: 0.8257 (pp30) cc_final: 0.8023 (pp30)
REVERT: B   18 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8005 (tm-30)
REVERT: B   19 LEU cc_start: 0.8988 (mm) cc_final: 0.8405 (mm)
REVERT: B   37 GLN cc_start: 0.8391 (mt0) cc_final: 0.8160 (mt0)
REVERT: B  191 ASP cc_start: 0.7960 (m-30) cc_final: 0.7487 (m-30)
REVERT: B  222 MET cc_start: 0.7776 (mmt) cc_final: 0.7489 (mmt)
REVERT: B  263 ASP cc_start: 0.8056 (t0) cc_final: 0.7505 (t0)
REVERT: B  291 LEU cc_start: 0.8529 (mp) cc_final: 0.8309 (mt)
REVERT: E   16 SER cc_start: 0.8414 (p) cc_final: 0.8148 (t)
REVERT: E   20 SER cc_start: 0.8223 (m) cc_final: 0.7882 (t)
REVERT: E   42 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8642 (mtpt)
REVERT: E   68 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8670 (p)
REVERT: E  139 VAL cc_start: 0.8482 (t) cc_final: 0.8207 (p)
REVERT: E  174 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8267 (tm)
REVERT: E  213 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8135 (p)
REVERT: R   36 ILE cc_start: 0.8525 (mp) cc_final: 0.8272 (mp)
REVERT: R   84 LEU cc_start: 0.8400 (mt) cc_final: 0.8188 (mp)
REVERT: R  101 VAL cc_start: 0.8580 (t) cc_final: 0.8327 (p)
REVERT: R  152 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8348 (tp)
  outliers start: 29
  outliers final: 20
  residues processed: 265
  average time/residue: 1.0254
  time to fit residues: 290.7969
Evaluate side-chains
  274 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 249
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LYS
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain E residue   42 LYS
Chi-restraints excluded: chain E residue   68 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  174 LEU
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain E residue  213 THR
Chi-restraints excluded: chain G residue   45 LYS
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  152 LEU
Chi-restraints excluded: chain R residue  180 THR
Chi-restraints excluded: chain R residue  203 LEU
Chi-restraints excluded: chain R residue  258 ILE
Chi-restraints excluded: chain R residue  275 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 29 optimal weight:    0.7980
   chunk 56 optimal weight:    0.2980
   chunk 88 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 64 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 ASN
B 225 GLN
B 264 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.116708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.107614 restraints weight = 12514.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 1.79
r_work: 0.3458 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3337 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.4087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8515  Z= 0.237
  Angle     :  0.583   9.545  11591  Z= 0.299
  Chirality :  0.044   0.306   1346
  Planarity :  0.004   0.046   1468
  Dihedral  :  4.110  19.851   1177
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 31.24 %
    Favored  : 65.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.26), residues: 1081
  helix:  2.64 (0.25), residues: 373
  sheet:  0.11 (0.32), residues: 277
  loop : -0.06 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 211 
 HIS   0.003   0.001   HIS A 329 
 PHE   0.038   0.002   PHE E  28 
 TYR   0.015   0.001   TYR E 190 
 ARG   0.009   0.001   ARG B  24 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 247
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8526 (mptm) cc_final: 0.8273 (mptm)
REVERT: A   21 LYS cc_start: 0.8590 (ttmm) cc_final: 0.8354 (ttmm)
REVERT: A   43 ASN cc_start: 0.8892 (p0) cc_final: 0.8623 (p0)
REVERT: A  192 ASP cc_start: 0.7537 (m-30) cc_final: 0.6907 (m-30)
REVERT: A  198 MET cc_start: 0.8711 (mtm) cc_final: 0.8411 (ttp)
REVERT: A  205 ARG cc_start: 0.8697 (mtp-110) cc_final: 0.8325 (mtm-85)
REVERT: A  267 LYS cc_start: 0.8368 (ttmm) cc_final: 0.8113 (ptpt)
REVERT: A  297 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6806 (mm-30)
REVERT: A  314 ASP cc_start: 0.8041 (m-30) cc_final: 0.7655 (m-30)
REVERT: A  340 ARG cc_start: 0.8577 (tpp-160) cc_final: 0.7573 (tpt170)
REVERT: B   11 GLN cc_start: 0.8298 (pp30) cc_final: 0.8026 (pp30)
REVERT: B   18 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8012 (tm-30)
REVERT: B   19 LEU cc_start: 0.8991 (mm) cc_final: 0.8430 (mm)
REVERT: B   37 GLN cc_start: 0.8393 (mt0) cc_final: 0.8173 (mt0)
REVERT: B   93 ASN cc_start: 0.8019 (m110) cc_final: 0.7769 (m110)
REVERT: B  191 ASP cc_start: 0.7917 (m-30) cc_final: 0.7417 (m-30)
REVERT: B  222 MET cc_start: 0.7775 (mmt) cc_final: 0.7498 (mmt)
REVERT: B  263 ASP cc_start: 0.8022 (t0) cc_final: 0.7527 (t0)
REVERT: B  291 LEU cc_start: 0.8514 (mp) cc_final: 0.8294 (mt)
REVERT: E   16 SER cc_start: 0.8425 (p) cc_final: 0.8166 (t)
REVERT: E   20 SER cc_start: 0.8247 (m) cc_final: 0.7905 (t)
REVERT: E   42 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8651 (mtpt)
REVERT: E   68 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8659 (p)
REVERT: E  139 VAL cc_start: 0.8471 (t) cc_final: 0.8190 (p)
REVERT: E  174 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8238 (tm)
REVERT: E  213 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8150 (p)
REVERT: R   36 ILE cc_start: 0.8515 (mp) cc_final: 0.8266 (mp)
REVERT: R   84 LEU cc_start: 0.8420 (mt) cc_final: 0.8207 (mp)
REVERT: R  101 VAL cc_start: 0.8571 (t) cc_final: 0.8330 (p)
REVERT: R  125 LEU cc_start: 0.8857 (mp) cc_final: 0.8655 (mt)
REVERT: R  152 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8346 (tp)
  outliers start: 28
  outliers final: 19
  residues processed: 262
  average time/residue: 1.0506
  time to fit residues: 294.5660
Evaluate side-chains
  271 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 247
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LYS
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  148 THR
Chi-restraints excluded: chain B residue  196 SER
Chi-restraints excluded: chain B residue  267 MET
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain E residue   42 LYS
Chi-restraints excluded: chain E residue   68 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  158 SER
Chi-restraints excluded: chain E residue  174 LEU
Chi-restraints excluded: chain E residue  184 SER
Chi-restraints excluded: chain E residue  213 THR
Chi-restraints excluded: chain G residue   45 LYS
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  152 LEU
Chi-restraints excluded: chain R residue  180 THR
Chi-restraints excluded: chain R residue  203 LEU
Chi-restraints excluded: chain R residue  258 ILE
Chi-restraints excluded: chain R residue  275 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 57 optimal weight:    0.6980
   chunk 66 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9980
   chunk 5 optimal weight:    0.3980
   chunk 91 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 97 optimal weight:    0.8980
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 GLN
B 264 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.117707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.108512 restraints weight = 12678.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 1.83
r_work: 0.3473 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.4198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8515  Z= 0.195
  Angle     :  0.574   9.866  11591  Z= 0.294
  Chirality :  0.043   0.306   1346
  Planarity :  0.004   0.045   1468
  Dihedral  :  4.034  19.379   1177
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 31.82 %
    Favored  : 65.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.26), residues: 1081
  helix:  2.73 (0.25), residues: 374
  sheet:  0.17 (0.32), residues: 272
  loop : -0.08 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 211 
 HIS   0.003   0.001   HIS A 329 
 PHE   0.038   0.002   PHE E  28 
 TYR   0.016   0.001   TYR E 190 
 ARG   0.012   0.001   ARG B  24 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7957.12 seconds
wall clock time: 140 minutes 0.06 seconds (8400.06 seconds total)