Starting phenix.real_space_refine
on Fri Feb 14 08:53:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ew2_28640/02_2025/8ew2_28640.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ew2_28640/02_2025/8ew2_28640.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ew2_28640/02_2025/8ew2_28640.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ew2_28640/02_2025/8ew2_28640.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ew2_28640/02_2025/8ew2_28640.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ew2_28640/02_2025/8ew2_28640.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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      44      5.16       5
     C    6516      2.51       5
     N    1832      2.21       5
     O    1948      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10340
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2585
          Classifications: {'peptide': 339}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 320}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2585
          Classifications: {'peptide': 339}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 320}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2585
          Classifications: {'peptide': 339}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 320}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2585
          Classifications: {'peptide': 339}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 320}
          Chain breaks: 1
  Time building chain proxies: 6.35, per 1000 atoms: 0.61
  Number of scatterers: 10340
  At special positions: 0
  Unit cell: (79.54, 97.58, 104.96, 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      44     16.00
     O    1948      8.00
     N    1832      7.00
     C    6516      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.85
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2488

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 8 sheets defined
      54.1% alpha, 12.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'B' and resid 8 through 23
    Processing helix  chain 'B' and resid 35 through 47
    Processing helix  chain 'B' and resid 51 through 64
    Processing helix  chain 'B' and resid 79 through 85
      removed outlier: 3.968A  pdb=" N   TYR B  84 " --> pdb=" O   HIS B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 100
    Processing helix  chain 'B' and resid 129 through 140
    Processing helix  chain 'B' and resid 159 through 180
    Processing helix  chain 'B' and resid 197 through 219
    Processing helix  chain 'B' and resid 222 through 226
    Processing helix  chain 'B' and resid 244 through 260
      removed outlier: 3.536A  pdb=" N   THR B 259 " --> pdb=" O   ALA B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 288
    Processing helix  chain 'B' and resid 302 through 314
      removed outlier: 6.790A  pdb=" N   SER B 308 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
      removed outlier: 5.051A  pdb=" N   ALA B 309 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 339
    Processing helix  chain 'A' and resid 8 through 23
    Processing helix  chain 'A' and resid 35 through 45
    Processing helix  chain 'A' and resid 51 through 64
      removed outlier: 3.585A  pdb=" N   ARG A  59 " --> pdb=" O   ARG A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 85
      removed outlier: 3.984A  pdb=" N   TYR A  84 " --> pdb=" O   HIS A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 100
    Processing helix  chain 'A' and resid 129 through 140
    Processing helix  chain 'A' and resid 159 through 180
    Processing helix  chain 'A' and resid 197 through 219
    Processing helix  chain 'A' and resid 222 through 226
    Processing helix  chain 'A' and resid 244 through 260
      removed outlier: 3.540A  pdb=" N   THR A 259 " --> pdb=" O   ALA A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 288
    Processing helix  chain 'A' and resid 302 through 312
      removed outlier: 6.840A  pdb=" N   SER A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   ALA A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 339
    Processing helix  chain 'C' and resid 8 through 23
    Processing helix  chain 'C' and resid 35 through 46
    Processing helix  chain 'C' and resid 51 through 64
    Processing helix  chain 'C' and resid 66 through 70
    Processing helix  chain 'C' and resid 79 through 85
    Processing helix  chain 'C' and resid 92 through 98
    Processing helix  chain 'C' and resid 129 through 140
    Processing helix  chain 'C' and resid 159 through 180
    Processing helix  chain 'C' and resid 197 through 219
    Processing helix  chain 'C' and resid 222 through 226
    Processing helix  chain 'C' and resid 244 through 260
      removed outlier: 3.552A  pdb=" N   THR C 259 " --> pdb=" O   ALA C 255 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 275 through 288
    Processing helix  chain 'C' and resid 302 through 314
      removed outlier: 6.514A  pdb=" N   SER C 308 " --> pdb=" O   ALA C 304 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   ALA C 309 " --> pdb=" O   LEU C 305 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 321 through 339
    Processing helix  chain 'D' and resid 8 through 23
    Processing helix  chain 'D' and resid 35 through 46
      removed outlier: 3.756A  pdb=" N   ILE D  46 " --> pdb=" O   ARG D  42 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 64
    Processing helix  chain 'D' and resid 79 through 85
      removed outlier: 3.968A  pdb=" N   TYR D  84 " --> pdb=" O   HIS D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 92 through 100
    Processing helix  chain 'D' and resid 129 through 140
    Processing helix  chain 'D' and resid 159 through 180
    Processing helix  chain 'D' and resid 197 through 219
    Processing helix  chain 'D' and resid 222 through 226
    Processing helix  chain 'D' and resid 244 through 260
      removed outlier: 3.525A  pdb=" N   THR D 259 " --> pdb=" O   ALA D 255 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 275 through 288
    Processing helix  chain 'D' and resid 302 through 314
      removed outlier: 6.314A  pdb=" N   SER D 308 " --> pdb=" O   ALA D 304 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   ALA D 309 " --> pdb=" O   LEU D 305 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 321 through 340
    Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 31
      removed outlier: 6.586A  pdb=" N   GLY B  28 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
      removed outlier: 5.661A  pdb=" N   VAL B  76 " --> pdb=" O   GLY B  28 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LEU B  30 " --> pdb=" O   VAL B  76 " (cutoff:3.500A)
      removed outlier: 5.778A  pdb=" N   LEU B  78 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      removed outlier: 7.269A  pdb=" N   VAL B 104 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)
      removed outlier: 5.852A  pdb=" N   ALA B 145 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   ILE B 106 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   TRP B 147 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   ASP B 143 " --> pdb=" O   VAL B 183 " (cutoff:3.500A)
      removed outlier: 8.013A  pdb=" N   ILE B 185 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ALA B 145 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   GLU B 187 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   TRP B 147 " --> pdb=" O   GLU B 187 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   GLU B 189 " --> pdb=" O   TRP B 147 " (cutoff:3.500A)
      removed outlier: 5.949A  pdb=" N   CYS B 149 " --> pdb=" O   GLU B 189 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   LEU B 191 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   LEU B 151 " --> pdb=" O   LEU B 191 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 114
    Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 31
      removed outlier: 6.805A  pdb=" N   GLY A  28 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   VAL A  76 " --> pdb=" O   GLY A  28 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   LEU A  30 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
      removed outlier: 5.693A  pdb=" N   LEU A  78 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 7.243A  pdb=" N   VAL A 104 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
      removed outlier: 5.867A  pdb=" N   ALA A 145 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
      removed outlier: 5.465A  pdb=" N   ILE A 106 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 6.103A  pdb=" N   TRP A 147 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   ASP A 143 " --> pdb=" O   VAL A 183 " (cutoff:3.500A)
      removed outlier: 8.022A  pdb=" N   ILE A 185 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   ALA A 145 " --> pdb=" O   ILE A 185 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   GLU A 187 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   TRP A 147 " --> pdb=" O   GLU A 187 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   GLU A 189 " --> pdb=" O   TRP A 147 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   CYS A 149 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   LEU A 191 " --> pdb=" O   CYS A 149 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   LEU A 151 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   LEU A 228 " --> pdb=" O   THR A 268 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114
    Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 31
      removed outlier: 6.959A  pdb=" N   GLY C  28 " --> pdb=" O   GLY C  74 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   VAL C  76 " --> pdb=" O   GLY C  28 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   LEU C  30 " --> pdb=" O   VAL C  76 " (cutoff:3.500A)
      removed outlier: 5.758A  pdb=" N   LEU C  78 " --> pdb=" O   LEU C  30 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ALA C 145 " --> pdb=" O   ILE C 185 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   GLU C 187 " --> pdb=" O   ALA C 145 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   TRP C 147 " --> pdb=" O   GLU C 187 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   GLU C 189 " --> pdb=" O   TRP C 147 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   CYS C 149 " --> pdb=" O   GLU C 189 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   LEU C 191 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   LEU C 151 " --> pdb=" O   LEU C 191 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   LEU C 228 " --> pdb=" O   THR C 268 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   VAL C 267 " --> pdb=" O   THR C 298 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   SER C 300 " --> pdb=" O   VAL C 267 " (cutoff:3.500A)
      removed outlier: 5.499A  pdb=" N   PHE C 269 " --> pdb=" O   SER C 300 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114
    Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 31
      removed outlier: 6.310A  pdb=" N   GLY D  28 " --> pdb=" O   GLY D  75 " (cutoff:3.500A)
      removed outlier: 7.732A  pdb=" N   ILE D  77 " --> pdb=" O   GLY D  28 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LEU D  30 " --> pdb=" O   ILE D  77 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   LEU D 228 " --> pdb=" O   THR D 268 " (cutoff:3.500A)
      removed outlier: 5.864A  pdb=" N   VAL D 267 " --> pdb=" O   THR D 298 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   SER D 300 " --> pdb=" O   VAL D 267 " (cutoff:3.500A)
      removed outlier: 5.384A  pdb=" N   PHE D 269 " --> pdb=" O   SER D 300 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114

    571 hydrogen bonds defined for protein.
    1656 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.44

  Time building geometry restraints manager: 3.21 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3441
        1.34 -     1.46: 1498
        1.46 -     1.57: 5536
        1.57 -     1.69: 1
        1.69 -     1.81: 56
  Bond restraints: 10532
  Sorted by residual:
  bond pdb=" CB  PRO D  71 "
       pdb=" CG  PRO D  71 "
    ideal  model  delta    sigma   weight residual
    1.492  1.600 -0.108 5.00e-02 4.00e+02 4.67e+00
  bond pdb=" C   ASN C  70 "
       pdb=" N   PRO C  71 "
    ideal  model  delta    sigma   weight residual
    1.331  1.348 -0.017 7.90e-03 1.60e+04 4.55e+00
  bond pdb=" C   ASN A  70 "
       pdb=" N   PRO A  71 "
    ideal  model  delta    sigma   weight residual
    1.335  1.350 -0.015 9.40e-03 1.13e+04 2.40e+00
  bond pdb=" CG1 ILE D  77 "
       pdb=" CD1 ILE D  77 "
    ideal  model  delta    sigma   weight residual
    1.513  1.458  0.055 3.90e-02 6.57e+02 2.00e+00
  bond pdb=" CB  GLN C  95 "
       pdb=" CG  GLN C  95 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 3.00e-02 1.11e+03 1.64e+00
  ... (remaining 10527 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 14040
        2.12 -     4.25: 199
        4.25 -     6.37: 25
        6.37 -     8.50: 3
        8.50 -    10.62: 1
  Bond angle restraints: 14268
  Sorted by residual:
  angle pdb=" CA  PRO D  71 "
        pdb=" N   PRO D  71 "
        pdb=" CD  PRO D  71 "
      ideal   model   delta    sigma   weight residual
     112.00  105.58    6.42 1.40e+00 5.10e-01 2.10e+01
  angle pdb=" N   VAL B  23 "
        pdb=" CA  VAL B  23 "
        pdb=" C   VAL B  23 "
      ideal   model   delta    sigma   weight residual
     106.21  110.54   -4.33 1.07e+00 8.73e-01 1.63e+01
  angle pdb=" C   THR A  51 "
        pdb=" N   GLU A  52 "
        pdb=" CA  GLU A  52 "
      ideal   model   delta    sigma   weight residual
     120.82  125.63   -4.81 1.50e+00 4.44e-01 1.03e+01
  angle pdb=" N   GLU A  49 "
        pdb=" CA  GLU A  49 "
        pdb=" C   GLU A  49 "
      ideal   model   delta    sigma   weight residual
     107.73  111.89   -4.16 1.34e+00 5.57e-01 9.63e+00
  angle pdb=" N   THR A  51 "
        pdb=" CA  THR A  51 "
        pdb=" C   THR A  51 "
      ideal   model   delta    sigma   weight residual
     110.35  114.64   -4.29 1.40e+00 5.10e-01 9.39e+00
  ... (remaining 14263 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 5508
       17.98 -    35.97: 694
       35.97 -    53.95: 167
       53.95 -    71.94: 39
       71.94 -    89.92: 12
  Dihedral angle restraints: 6420
    sinusoidal: 2540
      harmonic: 3880
  Sorted by residual:
  dihedral pdb=" CA  ALA A 304 "
           pdb=" C   ALA A 304 "
           pdb=" N   LEU A 305 "
           pdb=" CA  LEU A 305 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.78   18.22     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CB  GLU B 132 "
           pdb=" CG  GLU B 132 "
           pdb=" CD  GLU B 132 "
           pdb=" OE1 GLU B 132 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.92   89.92     1      3.00e+01 1.11e-03 1.07e+01
  dihedral pdb=" CA  ASP C  88 "
           pdb=" CB  ASP C  88 "
           pdb=" CG  ASP C  88 "
           pdb=" OD1 ASP C  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.17   56.17     1      2.00e+01 2.50e-03 1.06e+01
  ... (remaining 6417 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 936
       0.026 -    0.051: 393
       0.051 -    0.077: 158
       0.077 -    0.102: 99
       0.102 -    0.128: 42
  Chirality restraints: 1628
  Sorted by residual:
  chirality pdb=" CA  ILE B 190 "
            pdb=" N   ILE B 190 "
            pdb=" C   ILE B 190 "
            pdb=" CB  ILE B 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.07e-01
  chirality pdb=" CA  ILE D 182 "
            pdb=" N   ILE D 182 "
            pdb=" C   ILE D 182 "
            pdb=" CB  ILE D 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  chirality pdb=" CA  TYR C  84 "
            pdb=" N   TYR C  84 "
            pdb=" C   TYR C  84 "
            pdb=" CB  TYR C  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.73e-01
  ... (remaining 1625 not shown)

  Planarity restraints: 1848
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN D  70 "    0.044 5.00e-02 4.00e+02   6.38e-02 6.52e+00
        pdb=" N   PRO D  71 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO D  71 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO D  71 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 187 "   -0.033 5.00e-02 4.00e+02   4.98e-02 3.97e+00
        pdb=" N   PRO A 188 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 188 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 188 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A   8 "   -0.031 5.00e-02 4.00e+02   4.75e-02 3.61e+00
        pdb=" N   PRO A   9 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A   9 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A   9 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1845 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 662
        2.73 -     3.27: 10885
        3.27 -     3.82: 19395
        3.82 -     4.36: 23068
        4.36 -     4.90: 38736
  Nonbonded interactions: 92746
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 121 "
            pdb=" OG  SER A 159 "
     model   vdw
     2.188 3.040
  nonbonded pdb=" NZ  LYS B 146 "
            pdb=" OE1 GLU B 187 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" OE1 GLU A  81 "
            pdb=" NE2 GLN A  85 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" NZ  LYS C 207 "
            pdb=" O   SER D 217 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" O   GLN B  60 "
            pdb=" OG1 THR B  64 "
     model   vdw
     2.230 3.040
  ... (remaining 92741 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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:             0.900
  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:          0.390
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     26.170
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:2.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
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      :  0.004   0.108  10532  Z= 0.241
  Angle     :  0.626  10.619  14268  Z= 0.353
  Chirality :  0.040   0.128   1628
  Planarity :  0.005   0.064   1848
  Dihedral  : 17.049  89.921   3932
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 21.72 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.64 (0.24), residues: 1340
  helix:  1.69 (0.19), residues: 696
  sheet: -1.46 (0.38), residues: 192
  loop : -0.61 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 147 
 HIS   0.003   0.001   HIS B  80 
 PHE   0.010   0.001   PHE A  93 
 TYR   0.026   0.002   TYR B  58 
 ARG   0.006   0.001   ARG C  42 

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 116
  time to evaluate  : 1.210 
Fit side-chains
REVERT: C   84 TYR cc_start: 0.6279 (m-10) cc_final: 0.6030 (m-10)
  outliers start: 5
  outliers final: 4
  residues processed: 118
  average time/residue: 0.2447
  time to fit residues: 40.6119
Evaluate side-chains
  109 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  325 GLU
Chi-restraints excluded: chain C residue  338 CYS
Chi-restraints excluded: chain D residue   77 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    6.9990
   chunk 100 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 67 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   chunk 103 optimal weight:    7.9990
   chunk 40 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 77 optimal weight:    7.9990
   chunk 119 optimal weight:    4.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
B 231 ASN
B 324 GLN
** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  11 GLN
** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.144488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.113283 restraints weight = 13987.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 1.88
r_work: 0.3213 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.0705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  10532  Z= 0.285
  Angle     :  0.556   7.247  14268  Z= 0.286
  Chirality :  0.041   0.133   1628
  Planarity :  0.005   0.054   1848
  Dihedral  :  4.839  59.606   1460
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.07 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.63 (0.24), residues: 1340
  helix:  1.76 (0.19), residues: 696
  sheet: -1.32 (0.35), residues: 216
  loop : -0.81 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 147 
 HIS   0.003   0.001   HIS C  80 
 PHE   0.010   0.002   PHE A  93 
 TYR   0.020   0.002   TYR D 213 
 ARG   0.003   0.000   ARG B 148 

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 118
  time to evaluate  : 0.987 
Fit side-chains
REVERT: C   84 TYR cc_start: 0.6778 (m-10) cc_final: 0.6562 (m-10)
REVERT: C  303 ARG cc_start: 0.8137 (ptt180) cc_final: 0.7203 (ttt180)
REVERT: D   36 THR cc_start: 0.7279 (m) cc_final: 0.6827 (t)
REVERT: D  173 TYR cc_start: 0.9101 (OUTLIER) cc_final: 0.8831 (t80)
REVERT: D  295 TRP cc_start: 0.9080 (OUTLIER) cc_final: 0.7451 (m-90)
  outliers start: 36
  outliers final: 21
  residues processed: 141
  average time/residue: 0.2586
  time to fit residues: 50.1509
Evaluate side-chains
  131 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 1.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  338 CYS
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   66 ASP
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  321 LYS
Chi-restraints excluded: chain D residue  338 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 70 optimal weight:    0.0970
   chunk 11 optimal weight:    0.0000
   chunk 52 optimal weight:    2.9990
   chunk 116 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 114 optimal weight:    4.9990
   chunk 92 optimal weight:    2.9990
   chunk 101 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 118 optimal weight:    9.9990
   chunk 129 optimal weight:    3.9990
   overall best weight:    1.6188

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

Flipped N/Q/H residues before XYZ refinement:
B 324 GLN
A  11 GLN
** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 GLN
** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.143951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.112547 restraints weight = 14108.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 1.84
r_work: 0.3217 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3075 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.1031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  10532  Z= 0.280
  Angle     :  0.531   6.181  14268  Z= 0.272
  Chirality :  0.041   0.131   1628
  Planarity :  0.004   0.050   1848
  Dihedral  :  4.653  57.666   1457
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 17.70 %
    Favored  : 77.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.64 (0.23), residues: 1340
  helix:  1.83 (0.19), residues: 696
  sheet: -1.40 (0.34), residues: 216
  loop : -0.86 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 147 
 HIS   0.003   0.001   HIS C  80 
 PHE   0.011   0.001   PHE B 269 
 TYR   0.018   0.002   TYR C 213 
 ARG   0.003   0.000   ARG B 148 

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 128
  time to evaluate  : 1.175 
Fit side-chains
   revert: symmetry clash
REVERT: B  173 TYR cc_start: 0.9217 (OUTLIER) cc_final: 0.9014 (t80)
REVERT: B  295 TRP cc_start: 0.9042 (OUTLIER) cc_final: 0.8622 (m-90)
REVERT: A  106 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8766 (tt)
REVERT: A  173 TYR cc_start: 0.9206 (OUTLIER) cc_final: 0.9006 (t80)
REVERT: C  303 ARG cc_start: 0.8144 (ptt180) cc_final: 0.7245 (ttt180)
REVERT: D   36 THR cc_start: 0.7120 (m) cc_final: 0.6764 (t)
REVERT: D  173 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.8846 (t80)
REVERT: D  295 TRP cc_start: 0.9047 (OUTLIER) cc_final: 0.7380 (m-90)
  outliers start: 56
  outliers final: 35
  residues processed: 162
  average time/residue: 0.2909
  time to fit residues: 63.1114
Evaluate side-chains
  154 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 113
  time to evaluate  : 1.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  139 LYS
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  321 LYS
Chi-restraints excluded: chain B residue  324 GLN
Chi-restraints excluded: chain B residue  325 GLU
Chi-restraints excluded: chain A residue    4 HIS
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  338 CYS
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  278 GLU
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  321 LYS
Chi-restraints excluded: chain D residue  338 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 103 optimal weight:    7.9990
   chunk 60 optimal weight:    8.9990
   chunk 75 optimal weight:    8.9990
   chunk 111 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 120 optimal weight:    0.2980
   chunk 99 optimal weight:    3.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B 324 GLN
** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 166 ASN
** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.145653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.114120 restraints weight = 13962.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 1.90
r_work: 0.3236 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.1212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10532  Z= 0.205
  Angle     :  0.508   6.604  14268  Z= 0.258
  Chirality :  0.039   0.128   1628
  Planarity :  0.004   0.043   1848
  Dihedral  :  4.480  56.338   1457
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 19.53 %
    Favored  : 76.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.24), residues: 1340
  helix:  2.02 (0.19), residues: 696
  sheet: -1.42 (0.34), residues: 216
  loop : -0.83 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 147 
 HIS   0.004   0.001   HIS C  80 
 PHE   0.010   0.001   PHE D 144 
 TYR   0.015   0.001   TYR D 213 
 ARG   0.003   0.000   ARG A 303 

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 126
  time to evaluate  : 1.190 
Fit side-chains
REVERT: B  173 TYR cc_start: 0.9183 (OUTLIER) cc_final: 0.8973 (t80)
REVERT: B  293 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8760 (mtmm)
REVERT: B  295 TRP cc_start: 0.9027 (OUTLIER) cc_final: 0.8611 (m-90)
REVERT: A   84 TYR cc_start: 0.7833 (m-80) cc_final: 0.7573 (m-10)
REVERT: A  106 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8781 (tt)
REVERT: C   84 TYR cc_start: 0.6730 (m-10) cc_final: 0.6409 (m-10)
REVERT: C  303 ARG cc_start: 0.8122 (ptt180) cc_final: 0.7187 (ttt180)
REVERT: D   36 THR cc_start: 0.7003 (m) cc_final: 0.6733 (t)
REVERT: D  173 TYR cc_start: 0.9059 (OUTLIER) cc_final: 0.8790 (t80)
  outliers start: 43
  outliers final: 26
  residues processed: 150
  average time/residue: 0.2613
  time to fit residues: 53.6117
Evaluate side-chains
  148 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 117
  time to evaluate  : 1.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  232 MET
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  293 LYS
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  338 CYS
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  338 CYS
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  321 LYS
Chi-restraints excluded: chain D residue  338 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 28 optimal weight:    7.9990
   chunk 110 optimal weight:    3.9990
   chunk 97 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 130 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 117 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
B 324 GLN
** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 334 ASN
** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.144111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.112320 restraints weight = 13985.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 1.89
r_work: 0.3215 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.1386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  10532  Z= 0.253
  Angle     :  0.524   6.365  14268  Z= 0.267
  Chirality :  0.040   0.147   1628
  Planarity :  0.004   0.042   1848
  Dihedral  :  4.450  56.310   1457
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 18.70 %
    Favored  : 76.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.80 (0.24), residues: 1340
  helix:  2.02 (0.19), residues: 696
  sheet: -1.44 (0.34), residues: 216
  loop : -0.84 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D 147 
 HIS   0.003   0.001   HIS C  80 
 PHE   0.011   0.001   PHE C 144 
 TYR   0.019   0.002   TYR D 213 
 ARG   0.003   0.000   ARG A 303 

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 124
  time to evaluate  : 1.164 
Fit side-chains
REVERT: B  293 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8713 (mtmm)
REVERT: B  295 TRP cc_start: 0.9065 (OUTLIER) cc_final: 0.8761 (m-90)
REVERT: A  106 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8779 (tt)
REVERT: A  295 TRP cc_start: 0.9066 (OUTLIER) cc_final: 0.7303 (m-90)
REVERT: C  303 ARG cc_start: 0.8178 (ptt180) cc_final: 0.7283 (ttt180)
REVERT: D   36 THR cc_start: 0.6960 (m) cc_final: 0.6701 (t)
REVERT: D  173 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.8826 (t80)
REVERT: D  295 TRP cc_start: 0.9058 (OUTLIER) cc_final: 0.7254 (m-90)
  outliers start: 55
  outliers final: 39
  residues processed: 158
  average time/residue: 0.2436
  time to fit residues: 53.2539
Evaluate side-chains
  162 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 117
  time to evaluate  : 1.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  232 MET
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  293 LYS
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  321 LYS
Chi-restraints excluded: chain B residue  338 CYS
Chi-restraints excluded: chain A residue    4 HIS
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  338 CYS
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue  113 VAL
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  278 GLU
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  321 LYS
Chi-restraints excluded: chain D residue  329 LYS
Chi-restraints excluded: chain D residue  338 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 117 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 108 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 74 optimal weight:    0.2980
   chunk 23 optimal weight:    0.0870
   chunk 128 optimal weight:    1.9990
   chunk 75 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.6360

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

Flipped N/Q/H residues before XYZ refinement:
B 324 GLN
** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.148456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.118923 restraints weight = 14133.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 1.88
r_work: 0.3267 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10532  Z= 0.182
  Angle     :  0.493   6.818  14268  Z= 0.250
  Chirality :  0.039   0.142   1628
  Planarity :  0.004   0.042   1848
  Dihedral  :  4.274  54.649   1457
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 20.16 %
    Favored  : 76.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.97 (0.24), residues: 1340
  helix:  2.20 (0.19), residues: 696
  sheet: -1.47 (0.34), residues: 216
  loop : -0.79 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 295 
 HIS   0.003   0.000   HIS C  80 
 PHE   0.010   0.001   PHE C 144 
 TYR   0.013   0.001   TYR D 213 
 ARG   0.003   0.000   ARG A 303 

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 129
  time to evaluate  : 1.334 
Fit side-chains
REVERT: B  173 TYR cc_start: 0.9093 (OUTLIER) cc_final: 0.8861 (t80)
REVERT: B  293 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8696 (mtmm)
REVERT: B  295 TRP cc_start: 0.9029 (OUTLIER) cc_final: 0.8592 (m-90)
REVERT: A   83 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8492 (tp)
REVERT: A  106 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8781 (tt)
REVERT: A  332 LEU cc_start: 0.8577 (tt) cc_final: 0.8046 (mt)
REVERT: C   84 TYR cc_start: 0.6742 (m-10) cc_final: 0.6505 (m-10)
REVERT: C  303 ARG cc_start: 0.8197 (ptt180) cc_final: 0.7333 (ttt180)
REVERT: C  332 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8408 (mt)
REVERT: D  173 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.8773 (t80)
REVERT: D  199 LYS cc_start: 0.8525 (ttpp) cc_final: 0.8268 (mmmt)
  outliers start: 41
  outliers final: 27
  residues processed: 155
  average time/residue: 0.2523
  time to fit residues: 54.0059
Evaluate side-chains
  151 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 117
  time to evaluate  : 1.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  232 MET
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  293 LYS
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  325 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  278 GLU
Chi-restraints excluded: chain D residue  338 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 90 optimal weight:    0.7980
   chunk 101 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9980
   chunk 130 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   chunk 37 optimal weight:    0.0050
   chunk 122 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 94 optimal weight:    3.9990
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
B 324 GLN
A 231 ASN
A 274 GLN
** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.148503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.118688 restraints weight = 14302.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 1.89
r_work: 0.3276 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10532  Z= 0.188
  Angle     :  0.493   6.513  14268  Z= 0.250
  Chirality :  0.039   0.139   1628
  Planarity :  0.004   0.041   1848
  Dihedral  :  4.083  55.304   1456
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 19.98 %
    Favored  : 75.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.98 (0.24), residues: 1340
  helix:  2.26 (0.19), residues: 696
  sheet: -1.73 (0.36), residues: 176
  loop : -0.86 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 295 
 HIS   0.004   0.000   HIS C  80 
 PHE   0.010   0.001   PHE C 144 
 TYR   0.016   0.001   TYR C  84 
 ARG   0.003   0.000   ARG A 303 

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 132
  time to evaluate  : 1.309 
Fit side-chains
REVERT: B  293 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8716 (mtmm)
REVERT: B  295 TRP cc_start: 0.9039 (OUTLIER) cc_final: 0.8702 (m-90)
REVERT: A  106 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8789 (tt)
REVERT: A  247 GLU cc_start: 0.8250 (tm-30) cc_final: 0.8021 (tm-30)
REVERT: A  332 LEU cc_start: 0.8574 (tt) cc_final: 0.8073 (mt)
REVERT: C  303 ARG cc_start: 0.8195 (ptt180) cc_final: 0.7460 (ttt180)
REVERT: C  332 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8424 (mt)
REVERT: D  199 LYS cc_start: 0.8533 (ttpp) cc_final: 0.8299 (mmmt)
  outliers start: 49
  outliers final: 31
  residues processed: 162
  average time/residue: 0.2479
  time to fit residues: 55.8668
Evaluate side-chains
  158 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 123
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  232 MET
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  293 LYS
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  325 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  274 GLN
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  338 CYS
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue  113 VAL
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  321 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 110 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9990
   chunk 116 optimal weight:    0.6980
   chunk 63 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 89 optimal weight:    0.5980
   chunk 26 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 324 GLN
** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 231 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.148125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.118425 restraints weight = 14072.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 1.87
r_work: 0.3293 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3156 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10532  Z= 0.200
  Angle     :  0.508   6.440  14268  Z= 0.258
  Chirality :  0.039   0.138   1628
  Planarity :  0.004   0.040   1848
  Dihedral  :  4.078  55.390   1456
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 21.26 %
    Favored  : 75.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.98 (0.24), residues: 1340
  helix:  2.27 (0.19), residues: 696
  sheet: -1.73 (0.36), residues: 176
  loop : -0.86 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 147 
 HIS   0.007   0.001   HIS C  80 
 PHE   0.011   0.001   PHE C 144 
 TYR   0.018   0.001   TYR C  84 
 ARG   0.006   0.000   ARG C  68 

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 124
  time to evaluate  : 1.151 
Fit side-chains
REVERT: B  173 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.8881 (t80)
REVERT: B  293 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8722 (mtmm)
REVERT: B  295 TRP cc_start: 0.9035 (OUTLIER) cc_final: 0.8708 (m-90)
REVERT: A  106 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8817 (tt)
REVERT: A  189 GLU cc_start: 0.8279 (tp30) cc_final: 0.8075 (tp30)
REVERT: A  332 LEU cc_start: 0.8603 (tt) cc_final: 0.8101 (mt)
REVERT: C   84 TYR cc_start: 0.6621 (m-10) cc_final: 0.6376 (m-10)
REVERT: C  180 ASN cc_start: 0.8885 (m-40) cc_final: 0.8549 (m-40)
REVERT: C  303 ARG cc_start: 0.8198 (ptt180) cc_final: 0.7514 (ttt180)
REVERT: C  332 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8440 (mt)
REVERT: D  199 LYS cc_start: 0.8524 (ttpp) cc_final: 0.8323 (mmmt)
  outliers start: 36
  outliers final: 27
  residues processed: 147
  average time/residue: 0.2584
  time to fit residues: 52.3558
Evaluate side-chains
  153 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 121
  time to evaluate  : 1.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  293 LYS
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  325 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  338 CYS
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue  113 VAL
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  321 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 64 optimal weight:    8.9990
   chunk 90 optimal weight:    0.8980
   chunk 79 optimal weight:    0.8980
   chunk 59 optimal weight:    0.2980
   chunk 75 optimal weight:    5.9990
   chunk 60 optimal weight:    7.9990
   chunk 43 optimal weight:    2.9990
   chunk 104 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 324 GLN
** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 274 GLN
** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 231 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.148342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.118687 restraints weight = 14212.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 1.88
r_work: 0.3281 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10532  Z= 0.196
  Angle     :  0.505   6.425  14268  Z= 0.256
  Chirality :  0.039   0.137   1628
  Planarity :  0.004   0.039   1848
  Dihedral  :  4.046  55.594   1456
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 20.99 %
    Favored  : 75.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.99 (0.24), residues: 1340
  helix:  2.28 (0.19), residues: 696
  sheet: -1.76 (0.36), residues: 176
  loop : -0.84 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 147 
 HIS   0.006   0.001   HIS C  80 
 PHE   0.011   0.001   PHE C 144 
 TYR   0.018   0.001   TYR C  84 
 ARG   0.002   0.000   ARG A 303 

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 128
  time to evaluate  : 1.188 
Fit side-chains
   revert: symmetry clash
REVERT: B  173 TYR cc_start: 0.9119 (OUTLIER) cc_final: 0.8880 (t80)
REVERT: B  293 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8703 (mtmm)
REVERT: B  295 TRP cc_start: 0.9044 (OUTLIER) cc_final: 0.8787 (m-90)
REVERT: A  106 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8804 (tt)
REVERT: A  189 GLU cc_start: 0.8296 (tp30) cc_final: 0.8071 (tp30)
REVERT: A  295 TRP cc_start: 0.8983 (OUTLIER) cc_final: 0.7391 (m-90)
REVERT: A  332 LEU cc_start: 0.8608 (tt) cc_final: 0.8009 (mt)
REVERT: C   84 TYR cc_start: 0.6586 (m-10) cc_final: 0.6306 (m-10)
REVERT: C  180 ASN cc_start: 0.8881 (m-40) cc_final: 0.8569 (m-40)
REVERT: C  303 ARG cc_start: 0.8211 (ptt180) cc_final: 0.7506 (ttt180)
REVERT: C  332 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8432 (mt)
REVERT: D  199 LYS cc_start: 0.8516 (ttpp) cc_final: 0.8309 (mmmt)
  outliers start: 41
  outliers final: 30
  residues processed: 155
  average time/residue: 0.2587
  time to fit residues: 55.8634
Evaluate side-chains
  156 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 120
  time to evaluate  : 1.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  293 LYS
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  324 GLN
Chi-restraints excluded: chain B residue  325 GLU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  274 GLN
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  338 CYS
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue  113 VAL
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  321 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 40 optimal weight:    8.9990
   chunk 105 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 95 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 27 optimal weight:    6.9990
   chunk 100 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 324 GLN
** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 231 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.148298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.118904 restraints weight = 14107.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 1.86
r_work: 0.3277 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3137 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.1932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10532  Z= 0.205
  Angle     :  0.515   6.677  14268  Z= 0.260
  Chirality :  0.039   0.148   1628
  Planarity :  0.004   0.039   1848
  Dihedral  :  4.039  55.825   1456
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 21.81 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.99 (0.24), residues: 1340
  helix:  2.28 (0.19), residues: 696
  sheet: -1.77 (0.36), residues: 176
  loop : -0.84 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 147 
 HIS   0.006   0.001   HIS C  80 
 PHE   0.011   0.001   PHE C 144 
 TYR   0.018   0.002   TYR C  84 
 ARG   0.002   0.000   ARG C  42 

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 122
  time to evaluate  : 1.241 
Fit side-chains
   revert: symmetry clash
REVERT: B  173 TYR cc_start: 0.9129 (OUTLIER) cc_final: 0.8887 (t80)
REVERT: B  293 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8707 (mtmm)
REVERT: B  295 TRP cc_start: 0.9048 (OUTLIER) cc_final: 0.8796 (m-90)
REVERT: A  106 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8800 (tt)
REVERT: A  295 TRP cc_start: 0.8981 (OUTLIER) cc_final: 0.7394 (m-90)
REVERT: A  332 LEU cc_start: 0.8529 (tt) cc_final: 0.8031 (mt)
REVERT: C   84 TYR cc_start: 0.6564 (m-10) cc_final: 0.6319 (m-10)
REVERT: C  180 ASN cc_start: 0.8875 (m-40) cc_final: 0.8569 (m-40)
REVERT: C  303 ARG cc_start: 0.8207 (ptt180) cc_final: 0.7505 (ttt180)
REVERT: C  332 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8419 (mt)
REVERT: D  199 LYS cc_start: 0.8528 (ttpp) cc_final: 0.8310 (mmmt)
  outliers start: 35
  outliers final: 28
  residues processed: 146
  average time/residue: 0.2597
  time to fit residues: 52.0655
Evaluate side-chains
  153 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 119
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  293 LYS
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  324 GLN
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  338 CYS
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue  113 VAL
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  321 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 72 optimal weight:    0.5980
   chunk 124 optimal weight:    0.9990
   chunk 4 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0000
   chunk 123 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
B 324 GLN
** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 231 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.148578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.119087 restraints weight = 14010.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 1.86
r_work: 0.3297 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.1967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10532  Z= 0.194
  Angle     :  0.513   6.696  14268  Z= 0.259
  Chirality :  0.040   0.244   1628
  Planarity :  0.004   0.039   1848
  Dihedral  :  4.021  55.756   1456
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 21.44 %
    Favored  : 75.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.24), residues: 1340
  helix:  2.32 (0.19), residues: 696
  sheet: -1.78 (0.37), residues: 176
  loop : -0.83 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 295 
 HIS   0.006   0.000   HIS C  80 
 PHE   0.011   0.001   PHE C 144 
 TYR   0.017   0.001   TYR C  84 
 ARG   0.003   0.000   ARG A 303 

===============================================================================
Job complete
usr+sys time: 5178.64 seconds
wall clock time: 92 minutes 57.55 seconds (5577.55 seconds total)