Starting phenix.real_space_refine
on Sat Jun  7 02:52:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fn0_29302/06_2025/8fn0_29302.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fn0_29302/06_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_29302/06_2025/8fn0_29302.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fn0_29302/06_2025/8fn0_29302.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fn0_29302/06_2025/8fn0_29302.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fn0_29302/06_2025/8fn0_29302.cif"
  }
  resolution = 2.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 6}
          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: {'GLU:plan': 2, 'ARG:plan': 5, '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, 'ASP:plan': 2, 'ARG: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: 5.47, per 1000 atoms: 0.64
  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: 2.36
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 1.10
  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: 2.49

  Time building geometry restraints manager: 2.73 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:             1.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.940
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.980
-------------------------------------------------------------------------------
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 : 6.24
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (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
 TRP   0.022   0.003   TRP E 111 
 HIS   0.008   0.002   HIS C  91 
 PHE   0.023   0.003   PHE A 317 
 TYR   0.025   0.003   TYR E 102 
 ARG   0.015   0.001   ARG E  67 

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

*********************** 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  : 0.838 
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: 0.7436
  time to fit residues: 183.1072
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  : 0.979 
-------------------------------------------------------------------------------
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 92 optimal weight:    0.5980
   chunk 83 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 86 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 99 optimal weight:    6.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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  62 HIS
C  91 HIS
C 132 ASN
C 268 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 = 0.3822 r_free = 0.3822 target = 0.135675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.114210 restraints weight = 12536.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 2.13
r_work: 0.3401 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3244 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.1735

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= 0.170
  Angle     :  0.601   8.585  11804  Z= 0.325
  Chirality :  0.044   0.185   1371
  Planarity :  0.004   0.036   1486
  Dihedral  : 11.044 147.771   1225
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  :  7.95 %
    Favored  : 89.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.25), residues: 1098
  helix:  2.39 (0.26), residues: 364
  sheet:  1.16 (0.29), residues: 294
  loop :  0.46 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 321 
 HIS   0.006   0.001   HIS A 325 
 PHE   0.018   0.002   PHE C 199 
 TYR   0.025   0.002   TYR A 349 
 ARG   0.005   0.001   ARG C 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05218 (  446)
  hydrogen bonds       : angle       4.92589 ( 1254)
  SS BOND              : bond        0.00224 (    2)
  SS BOND              : angle       1.23141 (    4)
  covalent geometry    : bond        0.00379 ( 8680)
  covalent geometry    : angle       0.60079 (11800)

*********************** 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
  224 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 205
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
REVERT: A  128 PHE cc_start: 0.7001 (m-80) cc_final: 0.6712 (m-80)
REVERT: A  250 MET cc_start: 0.7118 (tpp) cc_final: 0.6799 (tpt)
REVERT: A  343 LEU cc_start: 0.7972 (tp) cc_final: 0.7679 (tt)
REVERT: A  350 PHE cc_start: 0.7120 (t80) cc_final: 0.6695 (t80)
REVERT: A  364 ILE cc_start: 0.8037 (mm) cc_final: 0.7823 (pp)
REVERT: C   37 ILE cc_start: 0.7964 (mt) cc_final: 0.7542 (pt)
REVERT: C   38 ASP cc_start: 0.8017 (m-30) cc_final: 0.7758 (m-30)
REVERT: C   49 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7601 (mpt-90)
REVERT: C   55 LEU cc_start: 0.8572 (mt) cc_final: 0.8366 (mt)
REVERT: C  158 VAL cc_start: 0.8412 (p) cc_final: 0.8028 (t)
REVERT: C  214 ARG cc_start: 0.7413 (mpt180) cc_final: 0.6795 (mpt180)
REVERT: B   66 ILE cc_start: 0.8113 (mt) cc_final: 0.7879 (mm)
REVERT: B  124 SER cc_start: 0.8514 (t) cc_final: 0.8234 (p)
REVERT: E   17 SER cc_start: 0.8089 (p) cc_final: 0.7846 (m)
REVERT: E   23 SER cc_start: 0.8250 (t) cc_final: 0.7968 (m)
REVERT: E   63 THR cc_start: 0.8353 (p) cc_final: 0.8147 (t)
REVERT: E   93 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8185 (tpp)
REVERT: E  129 THR cc_start: 0.8337 (m) cc_final: 0.7802 (p)
REVERT: E  192 SER cc_start: 0.8672 (t) cc_final: 0.8395 (p)
REVERT: E  211 ASP cc_start: 0.7951 (t0) cc_final: 0.7628 (t0)
  outliers start: 19
  outliers final: 12
  residues processed: 210
  average time/residue: 0.6891
  time to fit residues: 160.2023
Evaluate side-chains
  203 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 189
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
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   49 ARG
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  172 SER
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 106 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 103 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   chunk 109 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 97 optimal weight:    0.3980
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 241 ASN
C 340 ASN
B 202 ASN
E  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.135783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.114105 restraints weight = 12662.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 2.17
r_work: 0.3398 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8682  Z= 0.156
  Angle     :  0.565   8.686  11804  Z= 0.301
  Chirality :  0.043   0.257   1371
  Planarity :  0.004   0.041   1486
  Dihedral  : 10.665 147.990   1223
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 10.90 %
    Favored  : 86.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.25), residues: 1098
  helix:  2.61 (0.27), residues: 365
  sheet:  1.23 (0.29), residues: 293
  loop :  0.31 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 321 
 HIS   0.006   0.001   HIS A 325 
 PHE   0.016   0.002   PHE B 207 
 TYR   0.015   0.002   TYR E 178 
 ARG   0.008   0.001   ARG C 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04768 (  446)
  hydrogen bonds       : angle       4.66304 ( 1254)
  SS BOND              : bond        0.00126 (    2)
  SS BOND              : angle       0.90681 (    4)
  covalent geometry    : bond        0.00346 ( 8680)
  covalent geometry    : angle       0.56453 (11800)

*********************** 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
  220 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 199
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
REVERT: A  128 PHE cc_start: 0.7053 (m-80) cc_final: 0.6783 (m-80)
REVERT: A  250 MET cc_start: 0.7104 (tpp) cc_final: 0.6865 (tpt)
REVERT: C  158 VAL cc_start: 0.8457 (p) cc_final: 0.8079 (t)
REVERT: C  217 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7401 (ppp)
REVERT: C  219 ARG cc_start: 0.8311 (mtt-85) cc_final: 0.8068 (mtt90)
REVERT: B   66 ILE cc_start: 0.8184 (mt) cc_final: 0.7950 (mm)
REVERT: B  108 ASP cc_start: 0.7648 (t0) cc_final: 0.7394 (t0)
REVERT: B  124 SER cc_start: 0.8510 (t) cc_final: 0.8254 (p)
REVERT: E   17 SER cc_start: 0.8070 (p) cc_final: 0.7845 (m)
REVERT: E   23 SER cc_start: 0.8259 (t) cc_final: 0.7965 (m)
REVERT: E   93 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8087 (tpp)
REVERT: E  129 THR cc_start: 0.8337 (m) cc_final: 0.7792 (p)
REVERT: E  154 LEU cc_start: 0.8257 (tt) cc_final: 0.8040 (tp)
REVERT: E  192 SER cc_start: 0.8601 (t) cc_final: 0.8345 (p)
REVERT: E  200 PHE cc_start: 0.8506 (m-80) cc_final: 0.8144 (m-80)
REVERT: E  211 ASP cc_start: 0.7914 (t0) cc_final: 0.7593 (t0)
  outliers start: 21
  outliers final: 15
  residues processed: 206
  average time/residue: 0.7344
  time to fit residues: 166.9023
Evaluate side-chains
  205 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 188
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  252 VAL
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  170 ASP
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   chunk 82 optimal weight:    0.6980
   chunk 78 optimal weight:    0.5980
   chunk 105 optimal weight:    0.3980
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 141 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.135925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.114284 restraints weight = 12675.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 2.17
r_work: 0.3401 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3244 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8682  Z= 0.147
  Angle     :  0.549   8.147  11804  Z= 0.293
  Chirality :  0.043   0.259   1371
  Planarity :  0.004   0.037   1486
  Dihedral  : 10.510 148.053   1223
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 12.37 %
    Favored  : 85.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.25), residues: 1098
  helix:  2.63 (0.27), residues: 365
  sheet:  1.22 (0.29), residues: 291
  loop :  0.18 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 135 
 HIS   0.005   0.001   HIS A 325 
 PHE   0.017   0.002   PHE B 146 
 TYR   0.014   0.001   TYR E 178 
 ARG   0.008   0.001   ARG C 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04553 (  446)
  hydrogen bonds       : angle       4.59629 ( 1254)
  SS BOND              : bond        0.00115 (    2)
  SS BOND              : angle       0.97113 (    4)
  covalent geometry    : bond        0.00328 ( 8680)
  covalent geometry    : angle       0.54864 (11800)

*********************** 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
  214 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 191
  time to evaluate  : 0.827 
Fit side-chains
REVERT: A  128 PHE cc_start: 0.7077 (m-80) cc_final: 0.6832 (m-80)
REVERT: A  250 MET cc_start: 0.7087 (tpp) cc_final: 0.6857 (tpt)
REVERT: C   49 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7505 (mpt-90)
REVERT: C  158 VAL cc_start: 0.8436 (p) cc_final: 0.8075 (t)
REVERT: C  217 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7374 (ppp)
REVERT: C  219 ARG cc_start: 0.8336 (mtt-85) cc_final: 0.8127 (mtt90)
REVERT: B   66 ILE cc_start: 0.8198 (mt) cc_final: 0.7954 (mm)
REVERT: B  108 ASP cc_start: 0.7630 (t0) cc_final: 0.7349 (t0)
REVERT: B  208 ASP cc_start: 0.8077 (m-30) cc_final: 0.7831 (m-30)
REVERT: E   17 SER cc_start: 0.8042 (p) cc_final: 0.7833 (m)
REVERT: E   23 SER cc_start: 0.8245 (t) cc_final: 0.7938 (m)
REVERT: E   93 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8086 (tpp)
REVERT: E  129 THR cc_start: 0.8351 (m) cc_final: 0.7780 (p)
REVERT: E  154 LEU cc_start: 0.8265 (tt) cc_final: 0.8050 (tp)
REVERT: E  192 SER cc_start: 0.8598 (t) cc_final: 0.8339 (p)
REVERT: E  200 PHE cc_start: 0.8483 (m-80) cc_final: 0.8223 (m-80)
REVERT: E  211 ASP cc_start: 0.7940 (t0) cc_final: 0.7578 (t0)
  outliers start: 23
  outliers final: 14
  residues processed: 198
  average time/residue: 0.7407
  time to fit residues: 161.5726
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  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain C residue   49 ARG
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  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  183 LEU
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:    0.0770
   chunk 77 optimal weight:    0.1980
   chunk 97 optimal weight:    0.7980
   chunk 13 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 101 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 89 optimal weight:    0.6980
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
B 141 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 = 0.3832 r_free = 0.3832 target = 0.136419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.114711 restraints weight = 12497.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 2.15
r_work: 0.3409 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.2714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8682  Z= 0.126
  Angle     :  0.527   8.519  11804  Z= 0.281
  Chirality :  0.042   0.257   1371
  Planarity :  0.004   0.037   1486
  Dihedral  : 10.407 148.153   1223
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 12.37 %
    Favored  : 84.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.26), residues: 1098
  helix:  2.68 (0.27), residues: 366
  sheet:  1.21 (0.30), residues: 289
  loop :  0.07 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 135 
 HIS   0.004   0.001   HIS A 325 
 PHE   0.022   0.002   PHE A 147 
 TYR   0.014   0.001   TYR E 178 
 ARG   0.007   0.000   ARG C 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04250 (  446)
  hydrogen bonds       : angle       4.48734 ( 1254)
  SS BOND              : bond        0.00059 (    2)
  SS BOND              : angle       0.76833 (    4)
  covalent geometry    : bond        0.00276 ( 8680)
  covalent geometry    : angle       0.52681 (11800)

*********************** 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
  205 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 181
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
REVERT: A  128 PHE cc_start: 0.7056 (m-80) cc_final: 0.6842 (m-80)
REVERT: A  250 MET cc_start: 0.7010 (tpp) cc_final: 0.6762 (tpt)
REVERT: A  259 VAL cc_start: 0.8268 (t) cc_final: 0.8023 (t)
REVERT: C   49 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7463 (mpt-90)
REVERT: C  158 VAL cc_start: 0.8448 (p) cc_final: 0.8089 (t)
REVERT: C  217 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7332 (ppp)
REVERT: B   66 ILE cc_start: 0.8202 (mt) cc_final: 0.7961 (mm)
REVERT: B  108 ASP cc_start: 0.7605 (t0) cc_final: 0.7296 (t0)
REVERT: B  224 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7483 (tp)
REVERT: E   23 SER cc_start: 0.8217 (t) cc_final: 0.7924 (m)
REVERT: E   93 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8076 (tpp)
REVERT: E  129 THR cc_start: 0.8337 (m) cc_final: 0.7770 (p)
REVERT: E  154 LEU cc_start: 0.8316 (tt) cc_final: 0.8108 (tp)
REVERT: E  192 SER cc_start: 0.8566 (t) cc_final: 0.8311 (p)
REVERT: E  211 ASP cc_start: 0.7894 (t0) cc_final: 0.7522 (t0)
  outliers start: 24
  outliers final: 11
  residues processed: 191
  average time/residue: 0.7217
  time to fit residues: 152.2467
Evaluate side-chains
  194 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 179
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
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   49 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  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  212 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 88 optimal weight:    0.5980
   chunk 66 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 25 optimal weight:    0.2980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
C 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.135800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.114049 restraints weight = 12459.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 2.13
r_work: 0.3406 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3248 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.2854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8682  Z= 0.137
  Angle     :  0.553   9.547  11804  Z= 0.291
  Chirality :  0.042   0.251   1371
  Planarity :  0.004   0.039   1486
  Dihedral  : 10.640 148.301   1223
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 13.51 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.25), residues: 1098
  helix:  2.56 (0.27), residues: 368
  sheet:  1.17 (0.30), residues: 289
  loop : -0.02 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.002   TRP A 135 
 HIS   0.005   0.001   HIS A 325 
 PHE   0.021   0.002   PHE A 147 
 TYR   0.013   0.001   TYR E 178 
 ARG   0.004   0.000   ARG F   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04274 (  446)
  hydrogen bonds       : angle       4.49776 ( 1254)
  SS BOND              : bond        0.00115 (    2)
  SS BOND              : angle       0.84040 (    4)
  covalent geometry    : bond        0.00304 ( 8680)
  covalent geometry    : angle       0.55296 (11800)

*********************** 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
  208 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 186
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
REVERT: A  128 PHE cc_start: 0.7060 (m-80) cc_final: 0.6859 (m-80)
REVERT: A  204 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6695 (tmt)
REVERT: A  259 VAL cc_start: 0.8291 (t) cc_final: 0.8037 (t)
REVERT: C   49 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7471 (mpt-90)
REVERT: C  137 ARG cc_start: 0.7620 (mmt-90) cc_final: 0.7360 (mtt-85)
REVERT: C  158 VAL cc_start: 0.8435 (p) cc_final: 0.8080 (t)
REVERT: C  219 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8287 (mtt-85)
REVERT: B  108 ASP cc_start: 0.7623 (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: 0.8376 (OUTLIER) cc_final: 0.8102 (tpp)
REVERT: E  110 PHE cc_start: 0.8522 (t80) cc_final: 0.8059 (t80)
REVERT: E  129 THR cc_start: 0.8349 (m) cc_final: 0.7772 (p)
REVERT: E  192 SER cc_start: 0.8553 (t) cc_final: 0.8295 (p)
REVERT: E  211 ASP cc_start: 0.7900 (t0) cc_final: 0.7532 (t0)
  outliers start: 22
  outliers final: 13
  residues processed: 193
  average time/residue: 0.7282
  time to fit residues: 155.4462
Evaluate side-chains
  202 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 185
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain C residue   37 ILE
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  219 ARG
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9980
   chunk 101 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9990
   chunk 73 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.137285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.115179 restraints weight = 12396.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 2.17
r_work: 0.3390 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.2979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8682  Z= 0.166
  Angle     :  0.567   8.922  11804  Z= 0.302
  Chirality :  0.043   0.250   1371
  Planarity :  0.004   0.039   1486
  Dihedral  : 10.678 148.484   1223
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 13.96 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.26), residues: 1098
  helix:  2.52 (0.27), residues: 367
  sheet:  1.05 (0.29), residues: 301
  loop : -0.08 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP A 135 
 HIS   0.006   0.001   HIS A 325 
 PHE   0.021   0.002   PHE B 146 
 TYR   0.012   0.001   TYR E 178 
 ARG   0.005   0.000   ARG F   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04436 (  446)
  hydrogen bonds       : angle       4.64955 ( 1254)
  SS BOND              : bond        0.00175 (    2)
  SS BOND              : angle       0.94993 (    4)
  covalent geometry    : bond        0.00380 ( 8680)
  covalent geometry    : angle       0.56727 (11800)

*********************** 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
  203 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 183
  time to evaluate  : 0.848 
Fit side-chains
REVERT: A  204 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.6681 (tmt)
REVERT: A  259 VAL cc_start: 0.8280 (t) cc_final: 0.8027 (t)
REVERT: C   49 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7435 (mpt-90)
REVERT: C  158 VAL cc_start: 0.8478 (p) cc_final: 0.8060 (t)
REVERT: C  219 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8311 (mtt-85)
REVERT: B  108 ASP cc_start: 0.7659 (t0) cc_final: 0.7322 (t0)
REVERT: B  115 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6970 (mmm)
REVERT: B  208 ASP cc_start: 0.8072 (m-30) cc_final: 0.7815 (m-30)
REVERT: E   23 SER cc_start: 0.8225 (t) cc_final: 0.7928 (m)
REVERT: E   93 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8179 (tpp)
REVERT: E  110 PHE cc_start: 0.8554 (t80) cc_final: 0.8124 (t80)
REVERT: E  129 THR cc_start: 0.8355 (m) cc_final: 0.7778 (p)
REVERT: E  192 SER cc_start: 0.8594 (t) cc_final: 0.8320 (p)
REVERT: E  211 ASP cc_start: 0.7897 (t0) cc_final: 0.7505 (t0)
  outliers start: 20
  outliers final: 13
  residues processed: 189
  average time/residue: 0.7541
  time to fit residues: 157.4395
Evaluate side-chains
  196 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 178
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain C residue   37 ILE
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  219 ARG
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 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 96 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 100 optimal weight:    0.3980
   chunk 29 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.137595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.115527 restraints weight = 12491.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 2.18
r_work: 0.3399 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.3078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8682  Z= 0.146
  Angle     :  0.569   9.634  11804  Z= 0.298
  Chirality :  0.042   0.240   1371
  Planarity :  0.004   0.039   1486
  Dihedral  : 10.519 148.852   1223
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 13.85 %
    Favored  : 83.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.26), residues: 1098
  helix:  2.51 (0.27), residues: 367
  sheet:  1.05 (0.29), residues: 301
  loop : -0.11 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.002   TRP A 135 
 HIS   0.005   0.001   HIS A 325 
 PHE   0.021   0.002   PHE B 207 
 TYR   0.013   0.001   TYR E 178 
 ARG   0.005   0.000   ARG F   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04266 (  446)
  hydrogen bonds       : angle       4.60486 ( 1254)
  SS BOND              : bond        0.00160 (    2)
  SS BOND              : angle       0.90320 (    4)
  covalent geometry    : bond        0.00330 ( 8680)
  covalent geometry    : angle       0.56932 (11800)

*********************** 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
  212 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 189
  time to evaluate  : 0.850 
Fit side-chains
REVERT: A  119 LEU cc_start: 0.8571 (mt) cc_final: 0.8362 (mp)
REVERT: A  204 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.6607 (tmt)
REVERT: A  259 VAL cc_start: 0.8286 (t) cc_final: 0.8020 (t)
REVERT: A  313 VAL cc_start: 0.7536 (OUTLIER) cc_final: 0.6785 (p)
REVERT: C   49 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7433 (mpt-90)
REVERT: C   98 SER cc_start: 0.8355 (p) cc_final: 0.7884 (t)
REVERT: C  158 VAL cc_start: 0.8476 (p) cc_final: 0.8045 (t)
REVERT: C  219 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8338 (mtt-85)
REVERT: B  108 ASP cc_start: 0.7647 (t0) cc_final: 0.7313 (t0)
REVERT: B  208 ASP cc_start: 0.8069 (m-30) cc_final: 0.7820 (m-30)
REVERT: E   23 SER cc_start: 0.8225 (t) cc_final: 0.7927 (m)
REVERT: E   93 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8100 (tpp)
REVERT: E  110 PHE cc_start: 0.8589 (t80) cc_final: 0.8172 (t80)
REVERT: E  192 SER cc_start: 0.8555 (t) cc_final: 0.8280 (p)
REVERT: E  211 ASP cc_start: 0.7902 (t0) cc_final: 0.7507 (t0)
  outliers start: 23
  outliers final: 14
  residues processed: 198
  average time/residue: 0.7734
  time to fit residues: 168.5214
Evaluate side-chains
  207 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 188
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ASP
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain C residue   49 ARG
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  219 ARG
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 107 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 78 optimal weight:    0.4980
   chunk 74 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 77 optimal weight:    0.6980
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.137711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.115510 restraints weight = 12517.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 2.19
r_work: 0.3400 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.3153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8682  Z= 0.140
  Angle     :  0.563   8.395  11804  Z= 0.297
  Chirality :  0.042   0.239   1371
  Planarity :  0.004   0.038   1486
  Dihedral  : 10.429 148.934   1223
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.30 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.26), residues: 1098
  helix:  2.51 (0.27), residues: 368
  sheet:  1.01 (0.29), residues: 301
  loop : -0.13 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.002   TRP A 135 
 HIS   0.004   0.001   HIS A 325 
 PHE   0.023   0.002   PHE B 207 
 TYR   0.013   0.001   TYR E 178 
 ARG   0.006   0.000   ARG F   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04215 (  446)
  hydrogen bonds       : angle       4.58362 ( 1254)
  SS BOND              : bond        0.00080 (    2)
  SS BOND              : angle       0.83415 (    4)
  covalent geometry    : bond        0.00314 ( 8680)
  covalent geometry    : angle       0.56323 (11800)

*********************** 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
  214 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 191
  time to evaluate  : 0.846 
Fit side-chains
REVERT: A  108 SER cc_start: 0.7821 (t) cc_final: 0.7529 (t)
REVERT: A  159 ASN cc_start: 0.8114 (m-40) cc_final: 0.7907 (m-40)
REVERT: A  204 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.6552 (tmt)
REVERT: A  241 ASN cc_start: 0.7556 (t0) cc_final: 0.7237 (t0)
REVERT: A  259 VAL cc_start: 0.8280 (t) cc_final: 0.8020 (t)
REVERT: A  313 VAL cc_start: 0.7518 (OUTLIER) cc_final: 0.6765 (p)
REVERT: C   49 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7422 (mpt-90)
REVERT: C   98 SER cc_start: 0.8368 (p) cc_final: 0.7900 (t)
REVERT: C  158 VAL cc_start: 0.8472 (p) cc_final: 0.8044 (t)
REVERT: C  219 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8338 (mtt-85)
REVERT: B  108 ASP cc_start: 0.7661 (t0) cc_final: 0.7313 (t0)
REVERT: B  208 ASP cc_start: 0.8083 (m-30) cc_final: 0.7843 (m-30)
REVERT: E   23 SER cc_start: 0.8217 (t) cc_final: 0.7923 (m)
REVERT: E   93 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8078 (tpp)
REVERT: E  110 PHE cc_start: 0.8553 (t80) cc_final: 0.8145 (t80)
REVERT: E  192 SER cc_start: 0.8577 (t) cc_final: 0.8302 (p)
REVERT: E  211 ASP cc_start: 0.7923 (t0) cc_final: 0.7512 (t0)
  outliers start: 23
  outliers final: 13
  residues processed: 202
  average time/residue: 0.7930
  time to fit residues: 177.0225
Evaluate side-chains
  209 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 191
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  171 ILE
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   49 ARG
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  219 ARG
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0870
   chunk 100 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   chunk 5 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0000
   overall best weight:    0.3962

-------------------------------------------------------------------------------
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 = 0.3852 r_free = 0.3852 target = 0.137967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.115962 restraints weight = 12439.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 2.16
r_work: 0.3427 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.054   8682  Z= 0.115
  Angle     :  0.545   8.301  11804  Z= 0.286
  Chirality :  0.042   0.238   1371
  Planarity :  0.004   0.041   1486
  Dihedral  : 10.162 148.945   1223
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.87 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.26), residues: 1098
  helix:  2.58 (0.27), residues: 368
  sheet:  1.09 (0.30), residues: 295
  loop : -0.17 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP A 135 
 HIS   0.004   0.001   HIS B  77 
 PHE   0.022   0.001   PHE B 207 
 TYR   0.014   0.001   TYR E 178 
 ARG   0.005   0.000   ARG F   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03923 (  446)
  hydrogen bonds       : angle       4.48008 ( 1254)
  SS BOND              : bond        0.00086 (    2)
  SS BOND              : angle       0.64258 (    4)
  covalent geometry    : bond        0.00248 ( 8680)
  covalent geometry    : angle       0.54499 (11800)

********************** 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
  213 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 192
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
REVERT: A  204 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.6516 (tmt)
REVERT: A  241 ASN cc_start: 0.7528 (t0) cc_final: 0.7215 (t0)
REVERT: A  259 VAL cc_start: 0.8269 (t) cc_final: 0.8005 (t)
REVERT: C   49 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7466 (mpt-90)
REVERT: C   98 SER cc_start: 0.8357 (p) cc_final: 0.7967 (t)
REVERT: C  158 VAL cc_start: 0.8468 (p) cc_final: 0.8043 (t)
REVERT: C  217 MET cc_start: 0.8317 (pmm) cc_final: 0.7773 (pmm)
REVERT: C  219 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8301 (mmt-90)
REVERT: C  325 MET cc_start: 0.8124 (tpp) cc_final: 0.7841 (tpt)
REVERT: B  108 ASP cc_start: 0.7630 (t0) cc_final: 0.7285 (t0)
REVERT: B  170 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.7160 (m-30)
REVERT: B  211 THR cc_start: 0.8168 (m) cc_final: 0.7958 (m)
REVERT: E   23 SER cc_start: 0.8187 (t) cc_final: 0.7900 (m)
REVERT: E   93 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.8073 (tpp)
REVERT: E  110 PHE cc_start: 0.8519 (t80) cc_final: 0.8102 (t80)
REVERT: E  115 THR cc_start: 0.8262 (t) cc_final: 0.8018 (t)
REVERT: E  129 THR cc_start: 0.8386 (m) cc_final: 0.7816 (p)
REVERT: E  192 SER cc_start: 0.8521 (t) cc_final: 0.8270 (p)
REVERT: E  211 ASP cc_start: 0.7848 (t0) cc_final: 0.7448 (t0)
  outliers start: 21
  outliers final: 11
  residues processed: 200
  average time/residue: 0.7844
  time to fit residues: 173.9427
Evaluate side-chains
  201 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 185
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   49 ARG
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  219 ARG
Chi-restraints excluded: chain C residue  234 PHE
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   93 MET
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 44 optimal weight:    0.5980
   chunk 96 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 48 optimal weight:    0.0870
   chunk 1 optimal weight:    0.6980
   chunk 88 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 82 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A 365 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 = 0.137157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.114892 restraints weight = 12621.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 2.20
r_work: 0.3409 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.3330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8682  Z= 0.132
  Angle     :  0.558   8.420  11804  Z= 0.293
  Chirality :  0.042   0.227   1371
  Planarity :  0.004   0.040   1486
  Dihedral  : 10.230 149.106   1223
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.00 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.26), residues: 1098
  helix:  2.57 (0.27), residues: 368
  sheet:  1.08 (0.30), residues: 295
  loop : -0.25 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP A 135 
 HIS   0.004   0.001   HIS B  77 
 PHE   0.026   0.002   PHE B 207 
 TYR   0.014   0.001   TYR E 178 
 ARG   0.006   0.000   ARG A 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04037 (  446)
  hydrogen bonds       : angle       4.53974 ( 1254)
  SS BOND              : bond        0.00079 (    2)
  SS BOND              : angle       0.82813 (    4)
  covalent geometry    : bond        0.00298 ( 8680)
  covalent geometry    : angle       0.55809 (11800)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6950.89 seconds
wall clock time: 120 minutes 4.96 seconds (7204.96 seconds total)