Starting phenix.real_space_refine
on Fri Aug 22 22:45:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fn0_29302/08_2025/8fn0_29302.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fn0_29302/08_2025/8fn0_29302.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fn0_29302/08_2025/8fn0_29302.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fn0_29302/08_2025/8fn0_29302.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fn0_29302/08_2025/8fn0_29302.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fn0_29302/08_2025/8fn0_29302.cif"
  }
  resolution = 2.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.025
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: 5
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    5431      2.51       5
     N    1424      2.21       5
     O    1589      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8502
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2074
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2074
          Classifications: {'peptide': 282}
          Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 28}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 272}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 163
          Unresolved non-hydrogen angles: 209
          Unresolved non-hydrogen dihedrals: 138
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'ASN:plan1': 2, 'TYR:plan': 3, 'PHE:plan': 4, 'HIS:plan': 2, 'GLU:plan': 1, 'ARG:plan': 6, 'ASP:plan': 3, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 105
    Chain: "F"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 58
          Classifications: {'peptide': 6}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 4}
    Chain: "C"
      Number of atoms: 2568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2568
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 28
    Chain: "D"
      Number of atoms: 378
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 378
          Classifications: {'peptide': 51}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 1635
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1635
          Classifications: {'peptide': 212}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 4, 'TRANS': 207}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 30
    Chain: "E"
      Number of atoms: 1756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1756
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 33
          Unusual residues: {'SRW': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.51, per 1000 atoms: 0.18
  Number of scatterers: 8502
  At special positions: 0
  Unit cell: (91.52, 117.92, 132.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      57     16.00
     F       1      9.00
     O    1589      8.00
     N    1424      7.00
     C    5431      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 142 " - pdb=" SG  CYS A 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 347.6 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2086

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 14 sheets defined
      37.7% alpha, 24.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 60 through 90
    Processing helix  chain 'A' and resid 101 through 129
      Proline residue:  A 122  - end of helix
    Processing helix  chain 'A' and resid 137 through 173
      removed outlier: 3.503A  pdb=" N   GLY A 141 " --> pdb=" O   PHE A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 181
      removed outlier: 3.768A  pdb=" N   THR A 179 " --> pdb=" O   PHE A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 202
    Processing helix  chain 'A' and resid 203 through 207
    Processing helix  chain 'A' and resid 230 through 246
    Processing helix  chain 'A' and resid 246 through 266
    Processing helix  chain 'A' and resid 302 through 334
      Proline residue:  A 323  - end of helix
    Processing helix  chain 'A' and resid 335 through 339
    Processing helix  chain 'A' and resid 340 through 373
      removed outlier: 3.859A  pdb=" N   SER A 362 " --> pdb=" O   PHE A 358 " (cutoff:3.500A)
      Proline residue:  A 366  - end of helix
    Processing helix  chain 'C' and resid 4 through 25
    Processing helix  chain 'C' and resid 29 through 37
      removed outlier: 4.496A  pdb=" N   THR C  34 " --> pdb=" O   SER C  31 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   ASN C  35 " --> pdb=" O   GLN C  32 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   ASN C  36 " --> pdb=" O   ILE C  33 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 128 through 132
      removed outlier: 3.992A  pdb=" N   GLY C 131 " --> pdb=" O   THR C 128 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   ASN C 132 " --> pdb=" O   ARG C 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 128 through 132'
    Processing helix  chain 'D' and resid 12 through 24
    Processing helix  chain 'D' and resid 29 through 44
    Processing helix  chain 'D' and resid 45 through 48
    Processing helix  chain 'B' and resid 3 through 28
    Processing helix  chain 'B' and resid 42 through 46
    Processing helix  chain 'B' and resid 91 through 95
      removed outlier: 4.366A  pdb=" N   HIS B  95 " --> pdb=" O   LYS B  91 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 91 through 95'
    Processing helix  chain 'B' and resid 96 through 98
      No H-bonds generated for 'chain 'B' and resid 96 through 98'
    Processing helix  chain 'B' and resid 116 through 127
    Processing helix  chain 'B' and resid 142 through 150
      removed outlier: 4.761A  pdb=" N   GLU B 148 " --> pdb=" O   ASP B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 181
    Processing helix  chain 'B' and resid 202 through 220
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 3.738A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 74 through 76
      No H-bonds generated for 'chain 'E' and resid 74 through 76'
    Processing helix  chain 'E' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 212
    Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51
      removed outlier: 6.812A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63
      removed outlier: 3.574A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.993A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 5.028A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   GLY C 116 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   ILE C 120 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   CYS C 121 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   GLU C 138 " --> pdb=" O   CYS C 121 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   ILE C 123 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ARG C 134 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151
      removed outlier: 3.622A  pdb=" N   CYS C 148 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   CYS C 166 " --> pdb=" O   THR C 179 " (cutoff:3.500A)
      removed outlier: 4.824A  pdb=" N   THR C 179 " --> pdb=" O   CYS C 166 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   LEU C 168 " --> pdb=" O   THR C 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192
      removed outlier: 3.601A  pdb=" N   SER C 189 " --> pdb=" O   GLY C 202 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   SER C 207 " --> pdb=" O   ALA C 203 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234
      removed outlier: 3.600A  pdb=" N   ALA C 231 " --> pdb=" O   GLY C 244 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   CYS C 250 " --> pdb=" O   THR C 263 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   THR C 263 " --> pdb=" O   CYS C 250 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   LEU C 252 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.677A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 6.040A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 51 through 52
      removed outlier: 6.263A  pdb=" N   VAL B  31 " --> pdb=" O   ARG B  79 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   PHE B  81 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   LEU B  33 " --> pdb=" O   PHE B  81 " (cutoff:3.500A)
      removed outlier: 9.437A  pdb=" N   ALA B 102 " --> pdb=" O   ASP B  30 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   LYS B  32 " --> pdb=" O   ALA B 102 " (cutoff:3.500A)
      removed outlier: 7.933A  pdb=" N   ILE B 104 " --> pdb=" O   LYS B  32 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   LEU B  34 " --> pdb=" O   ILE B 104 " (cutoff:3.500A)
      removed outlier: 7.729A  pdb=" N   CYS B 106 " --> pdb=" O   LEU B  34 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   LEU B  36 " --> pdb=" O   CYS B 106 " (cutoff:3.500A)
      removed outlier: 8.709A  pdb=" N   ASP B 108 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   ILE B 103 " --> pdb=" O   ILE B 137 " (cutoff:3.500A)
      removed outlier: 7.318A  pdb=" N   PHE B 139 " --> pdb=" O   ILE B 103 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   PHE B 105 " --> pdb=" O   PHE B 139 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   ASN B 141 " --> pdb=" O   PHE B 105 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   VAL B 107 " --> pdb=" O   ASN B 141 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.974A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 130
    Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136
      removed outlier: 6.360A  pdb=" N   LEU E 162 " --> pdb=" O   TYR E 178 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   TYR E 178 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 136
      removed outlier: 4.121A  pdb=" N   THR E 226 " --> pdb=" O   GLN E 219 " (cutoff:3.500A)

    450 hydrogen bonds defined for protein.
    1254 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: 1.12

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2374
        1.33 -     1.45: 1630
        1.45 -     1.57: 4594
        1.57 -     1.69: 0
        1.69 -     1.81: 82
  Bond restraints: 8680
  Sorted by residual:
  bond pdb=" N   LEU A 371 "
       pdb=" CA  LEU A 371 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 1.17e-02 7.31e+03 1.11e+01
  bond pdb=" N   VAL A 372 "
       pdb=" CA  VAL A 372 "
    ideal  model  delta    sigma   weight residual
    1.461  1.500 -0.039 1.19e-02 7.06e+03 1.08e+01
  bond pdb=" C   VAL E 135 "
       pdb=" N   PRO E 136 "
    ideal  model  delta    sigma   weight residual
    1.332  1.373 -0.041 1.33e-02 5.65e+03 9.54e+00
  bond pdb=" N   ILE A 364 "
       pdb=" CA  ILE A 364 "
    ideal  model  delta    sigma   weight residual
    1.459  1.500 -0.041 1.34e-02 5.57e+03 9.50e+00
  bond pdb=" N   VAL E 137 "
       pdb=" CA  VAL E 137 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.14e-02 7.69e+03 9.29e+00
  ... (remaining 8675 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 11209
        2.05 -     4.11: 536
        4.11 -     6.16: 38
        6.16 -     8.21: 10
        8.21 -    10.27: 7
  Bond angle restraints: 11800
  Sorted by residual:
  angle pdb=" CA  MET B 115 "
        pdb=" C   MET B 115 "
        pdb=" O   MET B 115 "
      ideal   model   delta    sigma   weight residual
     121.99  113.37    8.62 1.14e+00 7.69e-01 5.72e+01
  angle pdb=" N   PRO E 136 "
        pdb=" CA  PRO E 136 "
        pdb=" C   PRO E 136 "
      ideal   model   delta    sigma   weight residual
     111.11  100.84   10.27 1.59e+00 3.96e-01 4.17e+01
  angle pdb=" N   CYS B 222 "
        pdb=" CA  CYS B 222 "
        pdb=" C   CYS B 222 "
      ideal   model   delta    sigma   weight residual
     113.16  105.24    7.92 1.24e+00 6.50e-01 4.08e+01
  angle pdb=" CA  ILE A 364 "
        pdb=" CB  ILE A 364 "
        pdb=" CG1 ILE A 364 "
      ideal   model   delta    sigma   weight residual
     110.40  119.83   -9.43 1.70e+00 3.46e-01 3.07e+01
  angle pdb=" CA  ILE A 367 "
        pdb=" CB  ILE A 367 "
        pdb=" CG1 ILE A 367 "
      ideal   model   delta    sigma   weight residual
     110.40  119.82   -9.42 1.70e+00 3.46e-01 3.07e+01
  ... (remaining 11795 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.17: 5035
       29.17 -    58.35: 52
       58.35 -    87.52: 22
       87.52 -   116.70: 2
      116.70 -   145.87: 3
  Dihedral angle restraints: 5114
    sinusoidal: 1878
      harmonic: 3236
  Sorted by residual:
  dihedral pdb=" CB  CYS A 142 "
           pdb=" SG  CYS A 142 "
           pdb=" SG  CYS A 225 "
           pdb=" CB  CYS A 225 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  159.95  -66.95     1      1.00e+01 1.00e-02 5.84e+01
  dihedral pdb=" C25 SRW A 501 "
           pdb=" C24 SRW A 501 "
           pdb=" C26 SRW A 501 "
           pdb=" F1  SRW A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     106.02 -108.11 -145.87     1      3.00e+01 1.11e-03 1.95e+01
  dihedral pdb=" C14 SRW A 501 "
           pdb=" C24 SRW A 501 "
           pdb=" C26 SRW A 501 "
           pdb=" C25 SRW A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     110.71 -109.31 -139.98     1      3.00e+01 1.11e-03 1.88e+01
  ... (remaining 5111 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.990: 1368
       0.990 -    1.979: 2
       1.979 -    2.969: 0
       2.969 -    3.959: 0
       3.959 -    4.948: 1
  Chirality restraints: 1371
  Sorted by residual:
  chirality pdb=" C8  SRW A 501 "
            pdb=" C12 SRW A 501 "
            pdb=" C3  SRW A 501 "
            pdb=" C9  SRW A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.46    2.49   -4.95 2.00e-01 2.50e+01 6.12e+02
  chirality pdb=" CB  ILE A 367 "
            pdb=" CA  ILE A 367 "
            pdb=" CG1 ILE A 367 "
            pdb=" CG2 ILE A 367 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    0.82    1.83 2.00e-01 2.50e+01 8.34e+01
  chirality pdb=" CB  ILE A 364 "
            pdb=" CA  ILE A 364 "
            pdb=" CG1 ILE A 364 "
            pdb=" CG2 ILE A 364 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    0.82    1.82 2.00e-01 2.50e+01 8.30e+01
  ... (remaining 1368 not shown)

  Planarity restraints: 1486
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 122 "   -0.026 2.00e-02 2.50e+03   5.14e-02 2.64e+01
        pdb=" C   PRO A 122 "    0.089 2.00e-02 2.50e+03
        pdb=" O   PRO A 122 "   -0.033 2.00e-02 2.50e+03
        pdb=" N   VAL A 123 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 124 "    0.022 2.00e-02 2.50e+03   4.28e-02 1.83e+01
        pdb=" C   GLU A 124 "   -0.074 2.00e-02 2.50e+03
        pdb=" O   GLU A 124 "    0.028 2.00e-02 2.50e+03
        pdb=" N   LEU A 125 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO E 136 "   -0.020 2.00e-02 2.50e+03   4.08e-02 1.66e+01
        pdb=" C   PRO E 136 "    0.070 2.00e-02 2.50e+03
        pdb=" O   PRO E 136 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   VAL E 137 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 1483 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1449
        2.76 -     3.29: 8161
        3.29 -     3.83: 14101
        3.83 -     4.36: 16917
        4.36 -     4.90: 29644
  Nonbonded interactions: 70272
  Sorted by model distance:
  nonbonded pdb=" O   MET C 325 "
            pdb=" ND2 ASN C 340 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" OH  TYR A 154 "
            pdb=" OD1 ASN A 241 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" OE1 GLU C 130 "
            pdb=" NH2 ARG C 134 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" ND1 HIS D  44 "
            pdb=" OE2 GLU D  47 "
     model   vdw
     2.328 3.120
  nonbonded pdb=" NE  ARG E 148 "
            pdb=" O   THR E 198 "
     model   vdw
     2.339 3.120
  ... (remaining 70267 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.330
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   8682  Z= 0.290
  Angle     :  0.949  10.266  11804  Z= 0.612
  Chirality :  0.159   4.948   1371
  Planarity :  0.006   0.084   1486
  Dihedral  : 11.788 145.870   3022
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.36 %
    Favored  : 98.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.24), residues: 1098
  helix:  0.92 (0.25), residues: 373
  sheet:  1.03 (0.28), residues: 307
  loop :  0.65 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG E  67 
 TYR   0.025   0.003   TYR E 102 
 PHE   0.023   0.003   PHE A 317 
 TRP   0.022   0.003   TRP E 111 
 HIS   0.008   0.002   HIS C  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 ( 8680)
  covalent geometry    : angle       0.94799 (11800)
  SS BOND              : bond        0.00256 (    2)
  SS BOND              : angle       2.49987 (    4)
  hydrogen bonds       : bond        0.14148 (  446)
  hydrogen bonds       : angle       6.50132 ( 1254)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 223
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LEU cc_start: 0.7888 (mt) cc_final: 0.7675 (tm)
REVERT: A  238 ILE cc_start: 0.7891 (tp) cc_final: 0.7662 (tp)
REVERT: A  250 MET cc_start: 0.7103 (tpp) cc_final: 0.6826 (tpt)
REVERT: A  343 LEU cc_start: 0.8181 (tp) cc_final: 0.7864 (tt)
REVERT: A  350 PHE cc_start: 0.7245 (t80) cc_final: 0.6821 (t80)
REVERT: C   37 ILE cc_start: 0.8089 (mt) cc_final: 0.7822 (pt)
REVERT: C   38 ASP cc_start: 0.7789 (m-30) cc_final: 0.7575 (m-30)
REVERT: C  227 SER cc_start: 0.8406 (t) cc_final: 0.8106 (m)
REVERT: C  262 MET cc_start: 0.8018 (tpp) cc_final: 0.7713 (tpp)
REVERT: C  314 ARG cc_start: 0.8538 (ttm170) cc_final: 0.8186 (ttm170)
REVERT: B   32 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8572 (mtmp)
REVERT: B   66 ILE cc_start: 0.8160 (mt) cc_final: 0.7937 (mm)
REVERT: E   17 SER cc_start: 0.8268 (p) cc_final: 0.7995 (m)
REVERT: E   23 SER cc_start: 0.8303 (t) cc_final: 0.8043 (m)
REVERT: E   25 SER cc_start: 0.8304 (t) cc_final: 0.8079 (p)
REVERT: E  192 SER cc_start: 0.8549 (t) cc_final: 0.8330 (p)
REVERT: E  211 ASP cc_start: 0.7989 (t0) cc_final: 0.7692 (t0)
REVERT: E  218 MET cc_start: 0.8279 (ttp) cc_final: 0.7915 (ttp)
  outliers start: 1
  outliers final: 1
  residues processed: 223
  average time/residue: 0.2957
  time to fit residues: 72.7584
Evaluate side-chains
  187 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 186
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.5980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0040
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    6.9990
   chunk 106 optimal weight:    0.6980
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
A 257 ASN
C  62 HIS
C  91 HIS
C 132 ASN
B  70 HIS
B  95 HIS
B 128 ASN
B 141 ASN
B 201 ASN
B 202 ASN
E  77 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.136549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.114941 restraints weight = 12687.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 2.16
r_work: 0.3413 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.1714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8682  Z= 0.150
  Angle     :  0.585   8.357  11804  Z= 0.316
  Chirality :  0.043   0.192   1371
  Planarity :  0.004   0.035   1486
  Dihedral  : 10.979 147.525   1225
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  :  7.95 %
    Favored  : 90.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.97 (0.25), residues: 1098
  helix:  2.44 (0.26), residues: 364
  sheet:  1.21 (0.29), residues: 292
  loop :  0.50 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 137 
 TYR   0.026   0.002   TYR A 349 
 PHE   0.017   0.002   PHE C 199 
 TRP   0.020   0.002   TRP A 321 
 HIS   0.005   0.001   HIS D  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 8680)
  covalent geometry    : angle       0.58436 (11800)
  SS BOND              : bond        0.00188 (    2)
  SS BOND              : angle       1.12119 (    4)
  hydrogen bonds       : bond        0.05057 (  446)
  hydrogen bonds       : angle       4.88143 ( 1254)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 204
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 PHE cc_start: 0.7001 (m-80) cc_final: 0.6703 (m-80)
REVERT: A  250 MET cc_start: 0.7105 (tpp) cc_final: 0.6783 (tpt)
REVERT: A  343 LEU cc_start: 0.7964 (tp) cc_final: 0.7660 (tt)
REVERT: A  364 ILE cc_start: 0.8024 (mm) cc_final: 0.7800 (pp)
REVERT: C   37 ILE cc_start: 0.7938 (mt) cc_final: 0.7518 (pt)
REVERT: C   38 ASP cc_start: 0.7993 (m-30) cc_final: 0.7746 (m-30)
REVERT: C   55 LEU cc_start: 0.8567 (mt) cc_final: 0.8361 (mt)
REVERT: C  158 VAL cc_start: 0.8432 (p) cc_final: 0.8019 (t)
REVERT: C  214 ARG cc_start: 0.7397 (mpt180) cc_final: 0.6784 (mpt180)
REVERT: B   66 ILE cc_start: 0.8118 (mt) cc_final: 0.7877 (mm)
REVERT: B   77 HIS cc_start: 0.8327 (t-170) cc_final: 0.8117 (t-170)
REVERT: B  124 SER cc_start: 0.8530 (t) cc_final: 0.8240 (p)
REVERT: E   17 SER cc_start: 0.8049 (p) cc_final: 0.7826 (m)
REVERT: E   23 SER cc_start: 0.8246 (t) cc_final: 0.7958 (m)
REVERT: E   93 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8206 (tpp)
REVERT: E  129 THR cc_start: 0.8333 (m) cc_final: 0.7805 (p)
REVERT: E  192 SER cc_start: 0.8674 (t) cc_final: 0.8399 (p)
REVERT: E  211 ASP cc_start: 0.7934 (t0) cc_final: 0.7620 (t0)
  outliers start: 17
  outliers final: 9
  residues processed: 208
  average time/residue: 0.3132
  time to fit residues: 71.7853
Evaluate side-chains
  198 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 188
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain C residue  184 THR
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  290 ASP
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  185 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 104 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 81 optimal weight:    0.4980
   chunk 53 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 71 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 105 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
C 340 ASN
E  77 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 = 0.135870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.114309 restraints weight = 12559.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 2.16
r_work: 0.3400 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.2191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8682  Z= 0.158
  Angle     :  0.567   8.540  11804  Z= 0.303
  Chirality :  0.043   0.258   1371
  Planarity :  0.004   0.041   1486
  Dihedral  : 10.654 148.003   1223
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 10.44 %
    Favored  : 86.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.02 (0.25), residues: 1098
  helix:  2.63 (0.27), residues: 365
  sheet:  1.27 (0.29), residues: 293
  loop :  0.35 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 219 
 TYR   0.015   0.002   TYR A 349 
 PHE   0.016   0.002   PHE C 199 
 TRP   0.027   0.002   TRP A 135 
 HIS   0.006   0.001   HIS A 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 8680)
  covalent geometry    : angle       0.56669 (11800)
  SS BOND              : bond        0.00233 (    2)
  SS BOND              : angle       1.10666 (    4)
  hydrogen bonds       : bond        0.04770 (  446)
  hydrogen bonds       : angle       4.66528 ( 1254)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 198
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 PHE cc_start: 0.7053 (m-80) cc_final: 0.6784 (m-80)
REVERT: A  250 MET cc_start: 0.7103 (tpp) cc_final: 0.6879 (tpt)
REVERT: A  355 ASN cc_start: 0.8610 (t0) cc_final: 0.8402 (m-40)
REVERT: C  158 VAL cc_start: 0.8447 (p) cc_final: 0.8060 (t)
REVERT: C  217 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7372 (ppp)
REVERT: C  219 ARG cc_start: 0.8351 (mtt-85) cc_final: 0.8083 (mtt90)
REVERT: B   66 ILE cc_start: 0.8184 (mt) cc_final: 0.7951 (mm)
REVERT: B  108 ASP cc_start: 0.7648 (t0) cc_final: 0.7394 (t0)
REVERT: B  124 SER cc_start: 0.8509 (t) cc_final: 0.8249 (p)
REVERT: E   17 SER cc_start: 0.8083 (p) cc_final: 0.7856 (m)
REVERT: E   23 SER cc_start: 0.8252 (t) cc_final: 0.7964 (m)
REVERT: E   93 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8082 (tpp)
REVERT: E  129 THR cc_start: 0.8317 (m) cc_final: 0.7789 (p)
REVERT: E  154 LEU cc_start: 0.8249 (tt) cc_final: 0.8022 (tp)
REVERT: E  192 SER cc_start: 0.8609 (t) cc_final: 0.8341 (p)
REVERT: E  200 PHE cc_start: 0.8512 (m-80) cc_final: 0.8151 (m-80)
REVERT: E  211 ASP cc_start: 0.7909 (t0) cc_final: 0.7602 (t0)
  outliers start: 24
  outliers final: 15
  residues processed: 206
  average time/residue: 0.3015
  time to fit residues: 68.4519
Evaluate side-chains
  207 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 190
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  290 ASP
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  115 MET
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  181 SER
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  172 SER
Chi-restraints excluded: chain E residue  212 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 69 optimal weight:    0.3980
   chunk 48 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   chunk 94 optimal weight:    0.0970
   chunk 42 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 85 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 52 optimal weight:    0.5980
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 241 ASN
** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  77 ASN
E 182 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.136724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.114986 restraints weight = 12759.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 2.19
r_work: 0.3412 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.2511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8682  Z= 0.129
  Angle     :  0.536   8.277  11804  Z= 0.285
  Chirality :  0.042   0.266   1371
  Planarity :  0.004   0.037   1486
  Dihedral  : 10.379 147.929   1223
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 12.94 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.25), residues: 1098
  helix:  2.68 (0.27), residues: 365
  sheet:  1.20 (0.29), residues: 293
  loop :  0.29 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 219 
 TYR   0.014   0.001   TYR E 178 
 PHE   0.020   0.002   PHE A 147 
 TRP   0.038   0.002   TRP A 135 
 HIS   0.004   0.001   HIS A 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 8680)
  covalent geometry    : angle       0.53627 (11800)
  SS BOND              : bond        0.00081 (    2)
  SS BOND              : angle       0.75477 (    4)
  hydrogen bonds       : bond        0.04399 (  446)
  hydrogen bonds       : angle       4.51251 ( 1254)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 181
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  128 PHE cc_start: 0.7103 (m-80) cc_final: 0.6837 (m-80)
REVERT: A  250 MET cc_start: 0.7059 (tpp) cc_final: 0.6838 (tpt)
REVERT: A  259 VAL cc_start: 0.8272 (t) cc_final: 0.8014 (t)
REVERT: C   78 LYS cc_start: 0.8556 (mptp) cc_final: 0.8328 (mptt)
REVERT: C  137 ARG cc_start: 0.7667 (mmt-90) cc_final: 0.7407 (mmt-90)
REVERT: C  158 VAL cc_start: 0.8487 (p) cc_final: 0.8109 (t)
REVERT: B   66 ILE cc_start: 0.8188 (mt) cc_final: 0.7935 (mm)
REVERT: B  108 ASP cc_start: 0.7632 (t0) cc_final: 0.7359 (t0)
REVERT: B  124 SER cc_start: 0.8516 (t) cc_final: 0.8260 (p)
REVERT: B  208 ASP cc_start: 0.8072 (m-30) cc_final: 0.7833 (m-30)
REVERT: E   23 SER cc_start: 0.8250 (t) cc_final: 0.7944 (m)
REVERT: E   93 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8094 (tpp)
REVERT: E  129 THR cc_start: 0.8324 (m) cc_final: 0.7791 (p)
REVERT: E  154 LEU cc_start: 0.8259 (tt) cc_final: 0.8043 (tp)
REVERT: E  192 SER cc_start: 0.8596 (t) cc_final: 0.8332 (p)
REVERT: E  200 PHE cc_start: 0.8470 (m-80) cc_final: 0.8181 (m-80)
REVERT: E  211 ASP cc_start: 0.7917 (t0) cc_final: 0.7591 (t0)
  outliers start: 21
  outliers final: 11
  residues processed: 185
  average time/residue: 0.3381
  time to fit residues: 68.4031
Evaluate side-chains
  192 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 180
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  290 ASP
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  181 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  212 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 91 optimal weight:    0.6980
   chunk 88 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 16 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.135516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.113421 restraints weight = 12628.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 2.18
r_work: 0.3388 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.2676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8682  Z= 0.163
  Angle     :  0.555   8.359  11804  Z= 0.296
  Chirality :  0.043   0.264   1371
  Planarity :  0.004   0.038   1486
  Dihedral  : 10.438 148.116   1223
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 12.49 %
    Favored  : 84.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.88 (0.25), residues: 1098
  helix:  2.61 (0.27), residues: 366
  sheet:  1.27 (0.30), residues: 284
  loop :  0.11 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F   9 
 TYR   0.013   0.001   TYR E 178 
 PHE   0.019   0.002   PHE A 147 
 TRP   0.049   0.002   TRP A 135 
 HIS   0.006   0.001   HIS A 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 8680)
  covalent geometry    : angle       0.55497 (11800)
  SS BOND              : bond        0.00233 (    2)
  SS BOND              : angle       0.95451 (    4)
  hydrogen bonds       : bond        0.04524 (  446)
  hydrogen bonds       : angle       4.58076 ( 1254)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 192
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A  128 PHE cc_start: 0.7078 (m-80) cc_final: 0.6842 (m-80)
REVERT: A  250 MET cc_start: 0.7050 (tpp) cc_final: 0.6809 (tpt)
REVERT: A  259 VAL cc_start: 0.8290 (t) cc_final: 0.8041 (t)
REVERT: C   78 LYS cc_start: 0.8566 (mptp) cc_final: 0.8333 (mptt)
REVERT: C  137 ARG cc_start: 0.7709 (mmt-90) cc_final: 0.7446 (mmt-90)
REVERT: C  158 VAL cc_start: 0.8458 (p) cc_final: 0.8100 (t)
REVERT: C  217 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.8017 (pmm)
REVERT: B   66 ILE cc_start: 0.8193 (mt) cc_final: 0.7943 (mm)
REVERT: B  108 ASP cc_start: 0.7648 (t0) cc_final: 0.7348 (t0)
REVERT: B  208 ASP cc_start: 0.8054 (m-30) cc_final: 0.7820 (m-30)
REVERT: B  224 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7470 (tp)
REVERT: E   23 SER cc_start: 0.8236 (t) cc_final: 0.7937 (m)
REVERT: E   93 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8077 (tpp)
REVERT: E  129 THR cc_start: 0.8322 (m) cc_final: 0.7773 (p)
REVERT: E  154 LEU cc_start: 0.8311 (tt) cc_final: 0.8096 (tp)
REVERT: E  192 SER cc_start: 0.8598 (t) cc_final: 0.8336 (p)
REVERT: E  211 ASP cc_start: 0.7941 (t0) cc_final: 0.7558 (t0)
  outliers start: 26
  outliers final: 16
  residues processed: 200
  average time/residue: 0.3089
  time to fit residues: 68.0464
Evaluate side-chains
  204 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 185
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  290 ASP
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  115 MET
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  172 SER
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain E residue  212 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0980
   chunk 66 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0370
   chunk 102 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 71 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:
** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 141 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.137180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.115414 restraints weight = 12570.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 2.17
r_work: 0.3412 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8682  Z= 0.121
  Angle     :  0.534   8.811  11804  Z= 0.283
  Chirality :  0.042   0.256   1371
  Planarity :  0.004   0.037   1486
  Dihedral  : 10.548 148.175   1223
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 13.85 %
    Favored  : 84.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.79 (0.25), residues: 1098
  helix:  2.59 (0.27), residues: 367
  sheet:  1.22 (0.30), residues: 285
  loop :  0.01 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F   9 
 TYR   0.014   0.001   TYR E 178 
 PHE   0.020   0.002   PHE B 146 
 TRP   0.051   0.002   TRP A 135 
 HIS   0.004   0.001   HIS A 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8680)
  covalent geometry    : angle       0.53374 (11800)
  SS BOND              : bond        0.00082 (    2)
  SS BOND              : angle       0.68924 (    4)
  hydrogen bonds       : bond        0.04149 (  446)
  hydrogen bonds       : angle       4.43018 ( 1254)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 180
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6447 (tmt)
REVERT: A  259 VAL cc_start: 0.8276 (t) cc_final: 0.8032 (t)
REVERT: C  158 VAL cc_start: 0.8483 (p) cc_final: 0.8040 (t)
REVERT: B  108 ASP cc_start: 0.7625 (t0) cc_final: 0.7315 (t0)
REVERT: E   23 SER cc_start: 0.8213 (t) cc_final: 0.7917 (m)
REVERT: E   93 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8062 (tpp)
REVERT: E  129 THR cc_start: 0.8323 (m) cc_final: 0.7764 (p)
REVERT: E  154 LEU cc_start: 0.8328 (tt) cc_final: 0.8120 (tp)
REVERT: E  192 SER cc_start: 0.8563 (t) cc_final: 0.8300 (p)
REVERT: E  200 PHE cc_start: 0.8298 (m-80) cc_final: 0.8026 (m-80)
REVERT: E  211 ASP cc_start: 0.7907 (t0) cc_final: 0.7528 (t0)
  outliers start: 18
  outliers final: 11
  residues processed: 186
  average time/residue: 0.3142
  time to fit residues: 64.5543
Evaluate side-chains
  191 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 178
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  290 ASP
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  172 SER
Chi-restraints excluded: chain E residue  212 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 70 optimal weight:    4.9990
   chunk 5 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   chunk 109 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   chunk 44 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.137142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.114951 restraints weight = 12589.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 2.20
r_work: 0.3394 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.2969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   8682  Z= 0.156
  Angle     :  0.562   9.133  11804  Z= 0.296
  Chirality :  0.043   0.253   1371
  Planarity :  0.004   0.039   1486
  Dihedral  : 10.626 148.420   1223
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.53 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.25), residues: 1098
  helix:  2.45 (0.27), residues: 368
  sheet:  1.15 (0.29), residues: 293
  loop : -0.05 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 219 
 TYR   0.013   0.001   TYR E 178 
 PHE   0.021   0.002   PHE B 146 
 TRP   0.049   0.002   TRP A 135 
 HIS   0.005   0.001   HIS A 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 8680)
  covalent geometry    : angle       0.56193 (11800)
  SS BOND              : bond        0.00130 (    2)
  SS BOND              : angle       0.90079 (    4)
  hydrogen bonds       : bond        0.04341 (  446)
  hydrogen bonds       : angle       4.56575 ( 1254)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 184
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6501 (tmt)
REVERT: A  259 VAL cc_start: 0.8265 (t) cc_final: 0.8027 (t)
REVERT: C  158 VAL cc_start: 0.8481 (p) cc_final: 0.8056 (t)
REVERT: B  108 ASP cc_start: 0.7665 (t0) cc_final: 0.7364 (t0)
REVERT: E   23 SER cc_start: 0.8235 (t) cc_final: 0.7931 (m)
REVERT: E   93 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8167 (tpp)
REVERT: E  110 PHE cc_start: 0.8548 (t80) cc_final: 0.8099 (t80)
REVERT: E  129 THR cc_start: 0.8342 (m) cc_final: 0.7768 (p)
REVERT: E  192 SER cc_start: 0.8565 (t) cc_final: 0.8290 (p)
REVERT: E  211 ASP cc_start: 0.7897 (t0) cc_final: 0.7506 (t0)
  outliers start: 16
  outliers final: 11
  residues processed: 190
  average time/residue: 0.2904
  time to fit residues: 61.1978
Evaluate side-chains
  196 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 183
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  290 ASP
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  172 SER
Chi-restraints excluded: chain E residue  212 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0370
   chunk 49 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 103 optimal weight:    0.4980
   chunk 26 optimal weight:    0.6980
   chunk 83 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 92 optimal weight:    0.1980
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.138596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.116676 restraints weight = 12455.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 2.18
r_work: 0.3417 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3260 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.3104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8682  Z= 0.118
  Angle     :  0.539   9.219  11804  Z= 0.283
  Chirality :  0.042   0.248   1371
  Planarity :  0.003   0.038   1486
  Dihedral  : 10.291 148.584   1223
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 15.10 %
    Favored  : 83.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.26), residues: 1098
  helix:  2.56 (0.27), residues: 368
  sheet:  1.16 (0.30), residues: 295
  loop : -0.05 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F   9 
 TYR   0.014   0.001   TYR E 178 
 PHE   0.021   0.002   PHE B 146 
 TRP   0.037   0.002   TRP A 135 
 HIS   0.004   0.001   HIS A 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 8680)
  covalent geometry    : angle       0.53854 (11800)
  SS BOND              : bond        0.00062 (    2)
  SS BOND              : angle       0.67533 (    4)
  hydrogen bonds       : bond        0.03989 (  446)
  hydrogen bonds       : angle       4.44059 ( 1254)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 186
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6482 (tmt)
REVERT: A  241 ASN cc_start: 0.7537 (t0) cc_final: 0.7220 (t0)
REVERT: A  259 VAL cc_start: 0.8270 (t) cc_final: 0.8019 (t)
REVERT: C   98 SER cc_start: 0.8367 (p) cc_final: 0.7906 (t)
REVERT: C  158 VAL cc_start: 0.8485 (p) cc_final: 0.8043 (t)
REVERT: C  264 TYR cc_start: 0.8462 (m-80) cc_final: 0.8235 (m-80)
REVERT: B  108 ASP cc_start: 0.7619 (t0) cc_final: 0.7310 (t0)
REVERT: E   23 SER cc_start: 0.8213 (t) cc_final: 0.7917 (m)
REVERT: E   93 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.8034 (tpp)
REVERT: E  110 PHE cc_start: 0.8523 (t80) cc_final: 0.8073 (t80)
REVERT: E  129 THR cc_start: 0.8331 (m) cc_final: 0.7754 (p)
REVERT: E  211 ASP cc_start: 0.7877 (t0) cc_final: 0.7470 (t0)
  outliers start: 15
  outliers final: 9
  residues processed: 193
  average time/residue: 0.3119
  time to fit residues: 66.3478
Evaluate side-chains
  191 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 180
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  172 SER
Chi-restraints excluded: chain E residue  212 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 90 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 105 optimal weight:    0.7980
   chunk 84 optimal weight:    8.9990
   chunk 92 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 16 optimal weight:    7.9990
   chunk 10 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 101 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 257 ASN
A 365 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.136160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.114103 restraints weight = 12552.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 2.19
r_work: 0.3397 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.3164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   8682  Z= 0.154
  Angle     :  0.561   9.338  11804  Z= 0.299
  Chirality :  0.043   0.229   1371
  Planarity :  0.004   0.039   1486
  Dihedral  : 10.444 148.980   1223
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 14.76 %
    Favored  : 82.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.26), residues: 1098
  helix:  2.53 (0.27), residues: 368
  sheet:  1.14 (0.30), residues: 295
  loop : -0.12 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F   9 
 TYR   0.013   0.001   TYR A 324 
 PHE   0.021   0.002   PHE B 207 
 TRP   0.041   0.002   TRP A 135 
 HIS   0.004   0.001   HIS B  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 8680)
  covalent geometry    : angle       0.56089 (11800)
  SS BOND              : bond        0.00168 (    2)
  SS BOND              : angle       0.93625 (    4)
  hydrogen bonds       : bond        0.04267 (  446)
  hydrogen bonds       : angle       4.62183 ( 1254)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 191
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6578 (tmt)
REVERT: A  241 ASN cc_start: 0.7507 (t0) cc_final: 0.7175 (t0)
REVERT: A  259 VAL cc_start: 0.8264 (t) cc_final: 0.8017 (t)
REVERT: A  313 VAL cc_start: 0.7502 (OUTLIER) cc_final: 0.6783 (p)
REVERT: C   98 SER cc_start: 0.8370 (p) cc_final: 0.7937 (t)
REVERT: C  158 VAL cc_start: 0.8489 (p) cc_final: 0.8058 (t)
REVERT: C  264 TYR cc_start: 0.8485 (m-80) cc_final: 0.8235 (m-80)
REVERT: C  276 VAL cc_start: 0.8652 (t) cc_final: 0.8367 (p)
REVERT: B  108 ASP cc_start: 0.7639 (t0) cc_final: 0.7312 (t0)
REVERT: B  170 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.7178 (m-30)
REVERT: E   23 SER cc_start: 0.8220 (t) cc_final: 0.7921 (m)
REVERT: E  110 PHE cc_start: 0.8593 (t80) cc_final: 0.8153 (t80)
REVERT: E  192 SER cc_start: 0.8636 (t) cc_final: 0.8260 (p)
REVERT: E  211 ASP cc_start: 0.7925 (t0) cc_final: 0.7495 (t0)
  outliers start: 24
  outliers final: 12
  residues processed: 202
  average time/residue: 0.3213
  time to fit residues: 71.5989
Evaluate side-chains
  201 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 186
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue  172 SER
Chi-restraints excluded: chain E residue  212 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 17 optimal weight:    6.9990
   chunk 85 optimal weight:    0.7980
   chunk 80 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 365 ASN
E 182 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.136541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.114437 restraints weight = 12403.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 2.18
r_work: 0.3389 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3230 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.3195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   8682  Z= 0.178
  Angle     :  0.589   9.278  11804  Z= 0.313
  Chirality :  0.044   0.228   1371
  Planarity :  0.004   0.040   1486
  Dihedral  : 10.557 149.340   1223
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.98 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.26), residues: 1098
  helix:  2.41 (0.27), residues: 367
  sheet:  1.06 (0.30), residues: 296
  loop : -0.22 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 219 
 TYR   0.016   0.002   TYR A 324 
 PHE   0.024   0.002   PHE B 207 
 TRP   0.047   0.002   TRP A 135 
 HIS   0.005   0.001   HIS A 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 8680)
  covalent geometry    : angle       0.58836 (11800)
  SS BOND              : bond        0.00394 (    2)
  SS BOND              : angle       1.02023 (    4)
  hydrogen bonds       : bond        0.04497 (  446)
  hydrogen bonds       : angle       4.71719 ( 1254)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 185
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.6600 (tmt)
REVERT: A  241 ASN cc_start: 0.7492 (t0) cc_final: 0.7140 (t0)
REVERT: A  259 VAL cc_start: 0.8276 (t) cc_final: 0.8024 (t)
REVERT: A  313 VAL cc_start: 0.7630 (OUTLIER) cc_final: 0.6894 (p)
REVERT: C  158 VAL cc_start: 0.8483 (p) cc_final: 0.8062 (t)
REVERT: C  264 TYR cc_start: 0.8481 (m-80) cc_final: 0.8266 (m-80)
REVERT: C  276 VAL cc_start: 0.8652 (t) cc_final: 0.8375 (p)
REVERT: B   99 ASP cc_start: 0.8089 (p0) cc_final: 0.7884 (p0)
REVERT: B  108 ASP cc_start: 0.7626 (t0) cc_final: 0.7298 (t0)
REVERT: B  115 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.6988 (mmm)
REVERT: B  170 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7237 (m-30)
REVERT: B  208 ASP cc_start: 0.8086 (m-30) cc_final: 0.7836 (m-30)
REVERT: E   23 SER cc_start: 0.8236 (t) cc_final: 0.7943 (m)
REVERT: E  110 PHE cc_start: 0.8589 (t80) cc_final: 0.8207 (t80)
REVERT: E  192 SER cc_start: 0.8647 (t) cc_final: 0.8278 (p)
REVERT: E  211 ASP cc_start: 0.7976 (t0) cc_final: 0.7547 (t0)
  outliers start: 19
  outliers final: 13
  residues processed: 194
  average time/residue: 0.3293
  time to fit residues: 70.1793
Evaluate side-chains
  201 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 184
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  371 LEU
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  115 MET
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain E residue   30 SER
Chi-restraints excluded: chain E residue  172 SER
Chi-restraints excluded: chain E residue  212 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 100 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   chunk 15 optimal weight:   10.0000
   chunk 108 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 89 optimal weight:    0.0770
   chunk 69 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0870
   overall best weight:    0.5316

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

Flipped N/Q/H residues before XYZ refinement:
A 325 HIS
A 365 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.141362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.118915 restraints weight = 12364.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 2.21
r_work: 0.3408 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.3304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   8682  Z= 0.130
  Angle     :  0.554   9.359  11804  Z= 0.294
  Chirality :  0.042   0.226   1371
  Planarity :  0.004   0.038   1486
  Dihedral  : 10.357 149.060   1223
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.87 %
    Favored  : 82.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.26), residues: 1098
  helix:  2.48 (0.27), residues: 367
  sheet:  1.11 (0.30), residues: 293
  loop : -0.26 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 219 
 TYR   0.014   0.001   TYR E 178 
 PHE   0.025   0.002   PHE B 207 
 TRP   0.040   0.002   TRP A 135 
 HIS   0.004   0.001   HIS B  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 8680)
  covalent geometry    : angle       0.55391 (11800)
  SS BOND              : bond        0.00245 (    2)
  SS BOND              : angle       0.80340 (    4)
  hydrogen bonds       : bond        0.04133 (  446)
  hydrogen bonds       : angle       4.58349 ( 1254)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2885.06 seconds
wall clock time: 49 minutes 49.31 seconds (2989.31 seconds total)