Starting phenix.real_space_refine
on Sat Jul 26 21:58:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vig_32008/07_2025/7vig_32008.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vig_32008/07_2025/7vig_32008.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/7vig_32008/07_2025/7vig_32008.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vig_32008/07_2025/7vig_32008.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vig_32008/07_2025/7vig_32008.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vig_32008/07_2025/7vig_32008.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=   0.051
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      65      5.16       5
     C    5692      2.51       5
     N    1508      2.21       5
     O    1654      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 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8920
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2601
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "E"
      Number of atoms: 1804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1804
          Classifications: {'peptide': 235}
          Link IDs: {'PTRANS': 10, 'TRANS': 224}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 2245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2245
          Classifications: {'peptide': 280}
          Link IDs: {'PTRANS': 6, 'TRANS': 273}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 1804
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 223, 1798
          Classifications: {'peptide': 223}
          Link IDs: {'PTRANS': 2, 'TRANS': 220}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 223, 1798
          Classifications: {'peptide': 223}
          Link IDs: {'PTRANS': 2, 'TRANS': 220}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 1820
    Chain: "F"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 30
          Unusual residues: {'7I4': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ACYS D 305 " occ=0.50
      ... (10 atoms not shown)
      pdb=" SG BCYS D 305 " occ=0.50
  Time building chain proxies: 6.21, per 1000 atoms: 0.70
  Number of scatterers: 8920
  At special positions: 0
  Unit cell: (92.13, 119.52, 128.65, 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      65     16.00
     F       1      9.00
     O    1654      8.00
     N    1508      7.00
     C    5692      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 184 " - pdb=" SG  CYS F 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 282 " - pdb=" SG  CYS F 287 " 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: 2.31
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2122

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 13 sheets defined
      38.5% alpha, 23.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 24
    Processing helix  chain 'A' and resid 28 through 33
    Processing helix  chain 'C' and resid 7 through 23
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 4.013A  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 87 through 91
      removed outlier: 3.933A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 220 through 224
      removed outlier: 3.744A  pdb=" N   VAL E 224 " --> pdb=" O   ALA E 221 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 33
      removed outlier: 3.779A  pdb=" N   THR F  32 " --> pdb=" O   HIS F  28 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 73
    Processing helix  chain 'F' and resid 78 through 105
    Processing helix  chain 'F' and resid 106 through 109
      removed outlier: 3.824A  pdb=" N   THR F 109 " --> pdb=" O   GLY F 106 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 106 through 109'
    Processing helix  chain 'F' and resid 113 through 148
      removed outlier: 3.922A  pdb=" N   MET F 124 " --> pdb=" O   ARG F 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 156 through 181
      removed outlier: 3.832A  pdb=" N   SER F 171 " --> pdb=" O   CYS F 167 " (cutoff:3.500A)
      Proline residue:  F 178  - end of helix
      removed outlier: 3.761A  pdb=" N   GLY F 181 " --> pdb=" O   LEU F 177 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 187 through 191
    Processing helix  chain 'F' and resid 199 through 235
      removed outlier: 3.726A  pdb=" N   LEU F 235 " --> pdb=" O   ARG F 231 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 250 through 282
      Proline residue:  F 271  - end of helix
      removed outlier: 3.890A  pdb=" N   VAL F 280 " --> pdb=" O   LEU F 276 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   GLY F 281 " --> pdb=" O   LEU F 277 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 295 through 314
      Proline residue:  F 308  - end of helix
    Processing helix  chain 'F' and resid 315 through 324
      removed outlier: 3.515A  pdb=" N   ARG F 324 " --> pdb=" O   ARG F 320 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 6 through 32
      removed outlier: 3.585A  pdb=" N   ARG D  32 " --> pdb=" O   GLU D  28 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 56
    Processing helix  chain 'D' and resid 207 through 216
      removed outlier: 4.743A  pdb=" N   ILE D 212 " --> pdb=" O   LYS D 209 " (cutoff:3.500A)
      removed outlier: 5.769A  pdb=" N   HIS D 213 " --> pdb=" O   LYS D 210 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 228 through 232
      removed outlier: 3.907A  pdb=" N   ASP D 231 " --> pdb=" O   SER D 228 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 241 through 255
      removed outlier: 3.569A  pdb=" N   GLU D 245 " --> pdb=" O   ASN D 241 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 270 through 278
    Processing helix  chain 'D' and resid 282 through 286
    Processing helix  chain 'D' and resid 295 through 310
      removed outlier: 3.740A  pdb=" N   LEU D 310 " --> pdb=" O   GLN D 306 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 330 through 351
    Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 50
      removed outlier: 5.462A  pdb=" N   THR A  46 " --> pdb=" O   ASN A 339 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   ASN A 339 " --> pdb=" O   THR A  46 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ARG A  48 " --> pdb=" O   ILE A 337 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 61
      removed outlier: 3.573A  pdb=" N   ALA A  59 " --> pdb=" O   ALA A  72 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   LYS A  77 " --> pdb=" O   SER A  73 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   LEU A  78 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   ALA A  91 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ILE A  80 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 104
      removed outlier: 4.156A  pdb=" N   GLY A 115 " --> pdb=" O   ILE A 119 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   ILE A 119 " --> pdb=" O   GLY A 115 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   ASN A 124 " --> pdb=" O   VAL A 134 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   VAL A 134 " --> pdb=" O   ASN A 124 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 150
      removed outlier: 4.044A  pdb=" N   THR A 164 " --> pdb=" O   SER A 160 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   ASP A 169 " --> pdb=" O   GLN A 175 " (cutoff:3.500A)
      removed outlier: 5.995A  pdb=" N   GLN A 175 " --> pdb=" O   ASP A 169 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 191
      removed outlier: 6.558A  pdb=" N   ALA A 207 " --> pdb=" O   THR A 220 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   THR A 220 " --> pdb=" O   ALA A 207 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   LEU A 209 " --> pdb=" O   ARG A 218 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 228 through 233
      removed outlier: 6.612A  pdb=" N   CYS A 249 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   THR A 262 " --> pdb=" O   CYS A 249 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   LEU A 251 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 277
      removed outlier: 3.643A  pdb=" N   SER A 274 " --> pdb=" O   GLY A 287 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   CYS A 293 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   VAL A 306 " --> pdb=" O   CYS A 293 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   VAL A 295 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12
      removed outlier: 6.773A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12
      removed outlier: 4.157A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141
      removed outlier: 3.517A  pdb=" N   THR E 213 " --> pdb=" O   SER E 206 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 149
      removed outlier: 6.417A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 185 through 191
      removed outlier: 6.625A  pdb=" N   ILE D 221 " --> pdb=" O   ILE D 265 " (cutoff:3.500A)
      removed outlier: 7.261A  pdb=" N   PHE D 267 " --> pdb=" O   ILE D 221 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   PHE D 223 " --> pdb=" O   PHE D 267 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   ASN D 269 " --> pdb=" O   PHE D 223 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   VAL D 225 " --> pdb=" O   ASN D 269 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   ILE D 264 " --> pdb=" O   TYR D 320 " (cutoff:3.500A)
      removed outlier: 7.963A  pdb=" N   HIS D 322 " --> pdb=" O   ILE D 264 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   LEU D 266 " --> pdb=" O   HIS D 322 " (cutoff:3.500A)

    470 hydrogen bonds defined for protein.
    1312 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: 2.63

  Time building geometry restraints manager: 2.68 seconds

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

  Histogram of bond lengths:
        1.15 -     1.29: 1435
        1.29 -     1.42: 2399
        1.42 -     1.55: 5170
        1.55 -     1.68: 3
        1.68 -     1.81: 92
  Bond restraints: 9099
  Sorted by residual:
  bond pdb=" C16 7I4 F 401 "
       pdb=" N17 7I4 F 401 "
    ideal  model  delta    sigma   weight residual
    1.441  1.155  0.286 2.00e-02 2.50e+03 2.05e+02
  bond pdb=" C18 7I4 F 401 "
       pdb=" C19 7I4 F 401 "
    ideal  model  delta    sigma   weight residual
    1.533  1.410  0.123 2.00e-02 2.50e+03 3.76e+01
  bond pdb=" C19 7I4 F 401 "
       pdb=" C23 7I4 F 401 "
    ideal  model  delta    sigma   weight residual
    1.537  1.417  0.120 2.00e-02 2.50e+03 3.59e+01
  bond pdb=" C11 7I4 F 401 "
       pdb=" C12 7I4 F 401 "
    ideal  model  delta    sigma   weight residual
    1.462  1.576 -0.114 2.00e-02 2.50e+03 3.23e+01
  bond pdb=" C08 7I4 F 401 "
       pdb=" C09 7I4 F 401 "
    ideal  model  delta    sigma   weight residual
    1.452  1.546 -0.094 2.00e-02 2.50e+03 2.22e+01
  ... (remaining 9094 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.15: 12217
        3.15 -     6.31: 79
        6.31 -     9.46: 11
        9.46 -    12.61: 4
       12.61 -    15.76: 2
  Bond angle restraints: 12313
  Sorted by residual:
  angle pdb=" C12 7I4 F 401 "
        pdb=" C11 7I4 F 401 "
        pdb=" N10 7I4 F 401 "
      ideal   model   delta    sigma   weight residual
     123.31  139.07  -15.76 3.00e+00 1.11e-01 2.76e+01
  angle pdb=" C11 7I4 F 401 "
        pdb=" C12 7I4 F 401 "
        pdb=" C26 7I4 F 401 "
      ideal   model   delta    sigma   weight residual
     119.29  132.36  -13.07 3.00e+00 1.11e-01 1.90e+01
  angle pdb=" CA  TYR E 235 "
        pdb=" CB  TYR E 235 "
        pdb=" CG  TYR E 235 "
      ideal   model   delta    sigma   weight residual
     113.90  106.09    7.81 1.80e+00 3.09e-01 1.88e+01
  angle pdb=" C15 7I4 F 401 "
        pdb=" C16 7I4 F 401 "
        pdb=" N17 7I4 F 401 "
      ideal   model   delta    sigma   weight residual
     110.91  122.57  -11.66 3.00e+00 1.11e-01 1.51e+01
  angle pdb=" C08 7I4 F 401 "
        pdb=" C09 7I4 F 401 "
        pdb=" N10 7I4 F 401 "
      ideal   model   delta    sigma   weight residual
     128.22  138.84  -10.62 3.00e+00 1.11e-01 1.25e+01
  ... (remaining 12308 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.28: 4899
       16.28 -    32.57: 402
       32.57 -    48.85: 90
       48.85 -    65.14: 11
       65.14 -    81.42: 12
  Dihedral angle restraints: 5414
    sinusoidal: 2125
      harmonic: 3289
  Sorted by residual:
  dihedral pdb=" CA  GLU E 234 "
           pdb=" C   GLU E 234 "
           pdb=" N   TYR E 235 "
           pdb=" CA  TYR E 235 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.89  -24.11     0      5.00e+00 4.00e-02 2.32e+01
  dihedral pdb=" CB  CYS F 184 "
           pdb=" SG  CYS F 184 "
           pdb=" SG  CYS F 191 "
           pdb=" CB  CYS F 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -126.20   40.20     1      1.00e+01 1.00e-02 2.27e+01
  dihedral pdb=" CA  MET D 240 "
           pdb=" C   MET D 240 "
           pdb=" N   ASN D 241 "
           pdb=" CA  ASN D 241 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.54  -20.46     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 5411 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.118: 1386
       0.118 -    0.236: 23
       0.236 -    0.354: 0
       0.354 -    0.472: 0
       0.472 -    0.590: 1
  Chirality restraints: 1410
  Sorted by residual:
  chirality pdb=" C19 7I4 F 401 "
            pdb=" C18 7I4 F 401 "
            pdb=" C20 7I4 F 401 "
            pdb=" C23 7I4 F 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.88   -2.29   -0.59 2.00e-01 2.50e+01 8.69e+00
  chirality pdb=" CB  ILE F  60 "
            pdb=" CA  ILE F  60 "
            pdb=" CG1 ILE F  60 "
            pdb=" CG2 ILE F  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.56e-01
  chirality pdb=" CG  LEU F 136 "
            pdb=" CB  LEU F 136 "
            pdb=" CD1 LEU F 136 "
            pdb=" CD2 LEU F 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.37e-01
  ... (remaining 1407 not shown)

  Planarity restraints: 1539
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 235 "    0.030 2.00e-02 2.50e+03   1.76e-02 6.23e+00
        pdb=" CG  TYR E 235 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 235 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 235 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 235 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 235 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 235 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR E 235 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR E 235 "   -0.033 5.00e-02 4.00e+02   4.93e-02 3.89e+00
        pdb=" N   PRO E 236 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO E 236 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO E 236 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR F 113 "    0.030 5.00e-02 4.00e+02   4.59e-02 3.37e+00
        pdb=" N   PRO F 114 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO F 114 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO F 114 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1536 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 812
        2.74 -     3.28: 8843
        3.28 -     3.82: 15048
        3.82 -     4.36: 18526
        4.36 -     4.90: 32670
  Nonbonded interactions: 75899
  Sorted by model distance:
  nonbonded pdb=" O   LEU F 174 "
            pdb=" OH  TYR F 202 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OD1 ASP D 251 "
            pdb=" ND2 ASN D 255 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" OE2 GLU D 318 "
            pdb=" OH  TYR D 320 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OD2 ASP A 227 "
            pdb=" NZ  LYS D 209 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" OG1 THR A 273 "
            pdb=" O   VAL A 314 "
     model   vdw
     2.224 3.040
  ... (remaining 75894 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:             1.620
  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:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.670
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
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      :  0.006   0.286   9103  Z= 0.273
  Angle     :  0.712  15.764  12321  Z= 0.348
  Chirality :  0.047   0.590   1410
  Planarity :  0.004   0.049   1539
  Dihedral  : 13.094  81.421   3280
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.25), residues: 1116
  helix:  1.92 (0.25), residues: 391
  sheet:  0.48 (0.31), residues: 274
  loop : -0.46 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  81 
 HIS   0.006   0.001   HIS A 141 
 PHE   0.014   0.001   PHE D 189 
 TYR   0.038   0.002   TYR E 235 
 ARG   0.005   0.000   ARG A 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14133 (  465)
  hydrogen bonds       : angle       5.63515 ( 1312)
  SS BOND              : bond        0.00173 (    4)
  SS BOND              : angle       1.17147 (    8)
  covalent geometry    : bond        0.00576 ( 9099)
  covalent geometry    : angle       0.71177 (12313)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 1.031 
Fit side-chains
REVERT: E   34 MET cc_start: 0.8934 (mmm) cc_final: 0.8672 (mmt)
REVERT: D  272 ASP cc_start: 0.7085 (m-30) cc_final: 0.6781 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 1.3144
  time to fit residues: 198.9304
Evaluate side-chains
  111 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    4.9990
   chunk 84 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 28 optimal weight:    0.6980
   chunk 56 optimal weight:    5.9990
   chunk 44 optimal weight:    0.0670
   chunk 87 optimal weight:    1.9990
   chunk 33 optimal weight:    9.9990
   chunk 52 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0170
   chunk 100 optimal weight:    0.3980
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
E  77 ASN
F 156 ASN
F 303 ASN
D 188 HIS
D 269 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.135134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.105410 restraints weight = 16476.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 2.31
r_work: 0.3052 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2906
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2906 r_free = 0.2906    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2906 r_free = 0.2906    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2906
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.1164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9103  Z= 0.125
  Angle     :  0.575   9.013  12321  Z= 0.292
  Chirality :  0.042   0.228   1410
  Planarity :  0.004   0.060   1539
  Dihedral  :  6.274  65.917   1243
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  :  8.70 %
    Favored  : 89.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.25), residues: 1116
  helix:  2.33 (0.25), residues: 386
  sheet:  0.70 (0.31), residues: 273
  loop : -0.45 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 168 
 HIS   0.003   0.001   HIS A 141 
 PHE   0.012   0.001   PHE A 233 
 TYR   0.028   0.001   TYR E 235 
 ARG   0.006   0.001   ARG F 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03637 (  465)
  hydrogen bonds       : angle       4.48642 ( 1312)
  SS BOND              : bond        0.00401 (    4)
  SS BOND              : angle       0.98274 (    8)
  covalent geometry    : bond        0.00277 ( 9099)
  covalent geometry    : angle       0.57494 (12313)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 1.044 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7538 (mtt-85)
REVERT: A  216 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8238 (ppp)
REVERT: A  218 ARG cc_start: 0.8267 (mtp85) cc_final: 0.8059 (mtp85)
REVERT: E  186 GLN cc_start: 0.8669 (tt0) cc_final: 0.8401 (tt0)
REVERT: E  230 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7730 (ttt)
REVERT: D  243 MET cc_start: 0.8249 (tpp) cc_final: 0.8027 (mmm)
REVERT: D  272 ASP cc_start: 0.7130 (m-30) cc_final: 0.6813 (m-30)
  outliers start: 15
  outliers final: 4
  residues processed: 132
  average time/residue: 1.0886
  time to fit residues: 154.8170
Evaluate side-chains
  113 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ARG
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  188 SER
Chi-restraints excluded: chain A residue  216 MET
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain E residue  230 MET
Chi-restraints excluded: chain F residue  113 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 101 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 77 optimal weight:    7.9990
   chunk 94 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
E  77 ASN
E 142 GLN
E 179 GLN
** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.131922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.100023 restraints weight = 25117.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 3.10
r_work: 0.2942 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2940
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2940
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.1377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9103  Z= 0.181
  Angle     :  0.582   7.715  12321  Z= 0.299
  Chirality :  0.043   0.259   1410
  Planarity :  0.004   0.058   1539
  Dihedral  :  5.970  49.668   1243
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 12.90 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.25), residues: 1116
  helix:  2.22 (0.25), residues: 392
  sheet:  0.52 (0.30), residues: 270
  loop : -0.64 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E  47 
 HIS   0.006   0.001   HIS A 141 
 PHE   0.012   0.001   PHE D 189 
 TYR   0.042   0.002   TYR E 235 
 ARG   0.007   0.001   ARG F 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03930 (  465)
  hydrogen bonds       : angle       4.38962 ( 1312)
  SS BOND              : bond        0.00296 (    4)
  SS BOND              : angle       1.18833 (    8)
  covalent geometry    : bond        0.00423 ( 9099)
  covalent geometry    : angle       0.58189 (12313)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 1.263 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ARG cc_start: 0.8058 (mtp85) cc_final: 0.7288 (mpt180)
REVERT: A  216 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8129 (ppp)
REVERT: E  186 GLN cc_start: 0.8707 (tt0) cc_final: 0.8467 (tt0)
REVERT: E  230 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8041 (ttt)
REVERT: F  174 LEU cc_start: 0.7287 (tt) cc_final: 0.7052 (tm)
REVERT: D  242 ARG cc_start: 0.7718 (mtt90) cc_final: 0.7481 (mtp85)
REVERT: D  272 ASP cc_start: 0.7109 (m-30) cc_final: 0.6676 (m-30)
  outliers start: 21
  outliers final: 9
  residues processed: 117
  average time/residue: 1.1602
  time to fit residues: 145.6063
Evaluate side-chains
  114 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  216 MET
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain E residue  230 MET
Chi-restraints excluded: chain F residue  108 THR
Chi-restraints excluded: chain F residue  113 THR
Chi-restraints excluded: chain F residue  164 ILE
Chi-restraints excluded: chain F residue  191 CYS
Chi-restraints excluded: chain D residue   18 MET
Chi-restraints excluded: chain D residue  316 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 99 optimal weight:    0.8980
   chunk 40 optimal weight:    0.5980
   chunk 108 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   chunk 90 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
E  77 ASN
D 244 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.133282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.103035 restraints weight = 17730.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 2.31
r_work: 0.3023 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2897 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2888
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2888 r_free = 0.2888    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2888 r_free = 0.2888    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2888
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.1574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9103  Z= 0.130
  Angle     :  0.525   7.342  12321  Z= 0.274
  Chirality :  0.042   0.236   1410
  Planarity :  0.004   0.058   1539
  Dihedral  :  5.398  41.320   1243
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.33 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.25), residues: 1116
  helix:  2.47 (0.25), residues: 387
  sheet:  0.61 (0.31), residues: 271
  loop : -0.56 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 168 
 HIS   0.003   0.001   HIS A 141 
 PHE   0.015   0.001   PHE D 189 
 TYR   0.038   0.001   TYR E 235 
 ARG   0.008   0.000   ARG F 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03531 (  465)
  hydrogen bonds       : angle       4.24068 ( 1312)
  SS BOND              : bond        0.00272 (    4)
  SS BOND              : angle       0.99147 (    8)
  covalent geometry    : bond        0.00297 ( 9099)
  covalent geometry    : angle       0.52416 (12313)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 1.001 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7633 (mpt-90)
REVERT: A   45 ARG cc_start: 0.8044 (mtp85) cc_final: 0.7154 (mpt180)
REVERT: E  186 GLN cc_start: 0.8664 (tt0) cc_final: 0.8460 (tt0)
REVERT: F  174 LEU cc_start: 0.7170 (tt) cc_final: 0.6923 (tm)
REVERT: F  302 LEU cc_start: 0.7760 (mp) cc_final: 0.7424 (mp)
REVERT: F  318 MET cc_start: 0.8112 (tpt) cc_final: 0.7887 (tpt)
REVERT: D  272 ASP cc_start: 0.7108 (m-30) cc_final: 0.6820 (m-30)
  outliers start: 20
  outliers final: 10
  residues processed: 121
  average time/residue: 1.1159
  time to fit residues: 145.2254
Evaluate side-chains
  117 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ARG
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain F residue  108 THR
Chi-restraints excluded: chain F residue  113 THR
Chi-restraints excluded: chain F residue  164 ILE
Chi-restraints excluded: chain F residue  191 CYS
Chi-restraints excluded: chain D residue   18 MET
Chi-restraints excluded: chain D residue  316 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 99 optimal weight:    0.4980
   chunk 6 optimal weight:    0.7980
   chunk 72 optimal weight:    0.0980
   chunk 19 optimal weight:    0.0370
   chunk 46 optimal weight:    0.7980
   chunk 9 optimal weight:    0.2980
   chunk 58 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.3258

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

Flipped N/Q/H residues before XYZ refinement:
E  77 ASN
D 255 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.137587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.105922 restraints weight = 27441.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 3.02
r_work: 0.3042 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3032
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3032
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9103  Z= 0.095
  Angle     :  0.472   7.560  12321  Z= 0.251
  Chirality :  0.040   0.199   1410
  Planarity :  0.004   0.058   1539
  Dihedral  :  4.686  34.467   1243
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 14.64 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.25), residues: 1116
  helix:  2.64 (0.25), residues: 387
  sheet:  0.63 (0.31), residues: 258
  loop : -0.44 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 168 
 HIS   0.002   0.000   HIS E 167 
 PHE   0.013   0.001   PHE D 189 
 TYR   0.032   0.001   TYR E 235 
 ARG   0.008   0.000   ARG F 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03156 (  465)
  hydrogen bonds       : angle       4.04961 ( 1312)
  SS BOND              : bond        0.00226 (    4)
  SS BOND              : angle       0.80658 (    8)
  covalent geometry    : bond        0.00204 ( 9099)
  covalent geometry    : angle       0.47147 (12313)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 1.048 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7697 (mpt-90)
REVERT: A   45 ARG cc_start: 0.7986 (mtp85) cc_final: 0.7267 (mpt180)
REVERT: A  196 ARG cc_start: 0.7941 (mtt-85) cc_final: 0.7387 (mmp80)
REVERT: C   21 MET cc_start: 0.7897 (mmm) cc_final: 0.7525 (tpp)
REVERT: E  186 GLN cc_start: 0.8519 (tt0) cc_final: 0.8303 (tt0)
REVERT: F  174 LEU cc_start: 0.7170 (tt) cc_final: 0.6944 (tm)
REVERT: F  177 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7800 (mt)
REVERT: F  292 ARG cc_start: 0.7545 (mpp80) cc_final: 0.6464 (mtm-85)
REVERT: F  302 LEU cc_start: 0.7843 (mp) cc_final: 0.7440 (mp)
REVERT: D   18 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8246 (ttt)
REVERT: D  272 ASP cc_start: 0.7068 (m-30) cc_final: 0.6837 (m-30)
  outliers start: 17
  outliers final: 7
  residues processed: 128
  average time/residue: 1.1444
  time to fit residues: 157.3557
Evaluate side-chains
  119 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ARG
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain F residue  108 THR
Chi-restraints excluded: chain F residue  113 THR
Chi-restraints excluded: chain F residue  177 LEU
Chi-restraints excluded: chain F residue  191 CYS
Chi-restraints excluded: chain D residue   18 MET
Chi-restraints excluded: chain D residue  316 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 77 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 70 optimal weight:    3.9990
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
A  87 ASN
** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.132250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.102964 restraints weight = 22545.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 2.70
r_work: 0.2938 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2946
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2946 r_free = 0.2946    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2946 r_free = 0.2946    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2946
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9103  Z= 0.174
  Angle     :  0.534   7.337  12321  Z= 0.284
  Chirality :  0.043   0.240   1410
  Planarity :  0.004   0.059   1539
  Dihedral  :  5.086  35.349   1243
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 15.05 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.25), residues: 1116
  helix:  2.50 (0.25), residues: 387
  sheet:  0.63 (0.32), residues: 267
  loop : -0.47 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E  47 
 HIS   0.006   0.001   HIS A 141 
 PHE   0.014   0.001   PHE D 189 
 TYR   0.043   0.002   TYR E 235 
 ARG   0.008   0.000   ARG F 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03689 (  465)
  hydrogen bonds       : angle       4.21571 ( 1312)
  SS BOND              : bond        0.00403 (    4)
  SS BOND              : angle       1.13171 (    8)
  covalent geometry    : bond        0.00408 ( 9099)
  covalent geometry    : angle       0.53327 (12313)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 1.060 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7499 (mpt-90)
REVERT: A   45 ARG cc_start: 0.7921 (mtp85) cc_final: 0.7077 (mpt180)
REVERT: A  196 ARG cc_start: 0.7916 (mtt-85) cc_final: 0.7299 (mmp80)
REVERT: A  213 ARG cc_start: 0.8627 (mmm-85) cc_final: 0.8364 (mmm-85)
REVERT: E  160 ARG cc_start: 0.7450 (ttp-170) cc_final: 0.7225 (mtm110)
REVERT: F  135 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7833 (mp)
REVERT: F  174 LEU cc_start: 0.7146 (tt) cc_final: 0.6925 (tm)
REVERT: F  235 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7699 (pp)
REVERT: D  272 ASP cc_start: 0.6915 (m-30) cc_final: 0.6518 (m-30)
  outliers start: 23
  outliers final: 12
  residues processed: 124
  average time/residue: 1.1459
  time to fit residues: 152.8109
Evaluate side-chains
  118 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ARG
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain F residue  108 THR
Chi-restraints excluded: chain F residue  113 THR
Chi-restraints excluded: chain F residue  135 LEU
Chi-restraints excluded: chain F residue  164 ILE
Chi-restraints excluded: chain F residue  191 CYS
Chi-restraints excluded: chain F residue  235 LEU
Chi-restraints excluded: chain F residue  309 ILE
Chi-restraints excluded: chain D residue   18 MET
Chi-restraints excluded: chain D residue  316 THR
Chi-restraints excluded: chain D residue  329 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 59 optimal weight:    3.9990
   chunk 95 optimal weight:    0.3980
   chunk 96 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 104 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  77 ASN
E 186 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.134462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.103268 restraints weight = 18819.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 2.47
r_work: 0.2974 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2860
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2860 r_free = 0.2860    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2860 r_free = 0.2860    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2860
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   9103  Z= 0.129
  Angle     :  0.505   7.424  12321  Z= 0.268
  Chirality :  0.042   0.252   1410
  Planarity :  0.004   0.055   1539
  Dihedral  :  4.858  33.769   1243
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 15.86 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.25), residues: 1116
  helix:  2.53 (0.25), residues: 387
  sheet:  0.64 (0.32), residues: 267
  loop : -0.44 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 168 
 HIS   0.003   0.001   HIS A 141 
 PHE   0.013   0.001   PHE D 189 
 TYR   0.026   0.001   TYR E 235 
 ARG   0.009   0.000   ARG F 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03465 (  465)
  hydrogen bonds       : angle       4.17713 ( 1312)
  SS BOND              : bond        0.00295 (    4)
  SS BOND              : angle       1.43183 (    8)
  covalent geometry    : bond        0.00301 ( 9099)
  covalent geometry    : angle       0.50406 (12313)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.843 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7527 (mpt-90)
REVERT: A   45 ARG cc_start: 0.8076 (mtp85) cc_final: 0.7175 (mpt180)
REVERT: A  196 ARG cc_start: 0.7953 (mtt-85) cc_final: 0.7205 (mmp80)
REVERT: F  135 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7968 (mp)
REVERT: F  174 LEU cc_start: 0.7112 (tt) cc_final: 0.6746 (tm)
REVERT: F  177 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7358 (mp)
REVERT: F  235 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7648 (pp)
REVERT: F  292 ARG cc_start: 0.7515 (mpp80) cc_final: 0.6360 (mtm-85)
REVERT: F  302 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7259 (mp)
REVERT: D  272 ASP cc_start: 0.7121 (m-30) cc_final: 0.6809 (m-30)
  outliers start: 21
  outliers final: 10
  residues processed: 123
  average time/residue: 1.1693
  time to fit residues: 154.0275
Evaluate side-chains
  120 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ARG
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain F residue  108 THR
Chi-restraints excluded: chain F residue  113 THR
Chi-restraints excluded: chain F residue  135 LEU
Chi-restraints excluded: chain F residue  177 LEU
Chi-restraints excluded: chain F residue  191 CYS
Chi-restraints excluded: chain F residue  235 LEU
Chi-restraints excluded: chain F residue  302 LEU
Chi-restraints excluded: chain F residue  309 ILE
Chi-restraints excluded: chain D residue   18 MET
Chi-restraints excluded: chain D residue  316 THR
Chi-restraints excluded: chain D residue  329 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 62 optimal weight:    8.9990
   chunk 100 optimal weight:    0.5980
   chunk 87 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9990
   chunk 52 optimal weight:    6.9990
   chunk 105 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0370
   chunk 45 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    0.6460

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

Flipped N/Q/H residues before XYZ refinement:
A  12 GLN
** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  77 ASN
** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 255 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.134902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.105472 restraints weight = 20138.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 2.46
r_work: 0.3001 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2871 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2874
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2874 r_free = 0.2874    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2874 r_free = 0.2874    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2874
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   9103  Z= 0.114
  Angle     :  0.495   7.432  12321  Z= 0.262
  Chirality :  0.041   0.280   1410
  Planarity :  0.004   0.058   1539
  Dihedral  :  4.608  31.224   1243
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.79 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.25), residues: 1116
  helix:  2.58 (0.25), residues: 387
  sheet:  0.65 (0.31), residues: 272
  loop : -0.35 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 168 
 HIS   0.003   0.001   HIS A 141 
 PHE   0.013   0.001   PHE D 189 
 TYR   0.027   0.001   TYR E 235 
 ARG   0.010   0.000   ARG F 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03329 (  465)
  hydrogen bonds       : angle       4.10315 ( 1312)
  SS BOND              : bond        0.00263 (    4)
  SS BOND              : angle       1.26568 (    8)
  covalent geometry    : bond        0.00264 ( 9099)
  covalent geometry    : angle       0.49368 (12313)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7658 (mpt-90)
REVERT: A   45 ARG cc_start: 0.8145 (mtp85) cc_final: 0.7301 (mpt180)
REVERT: A  196 ARG cc_start: 0.7979 (mtt-85) cc_final: 0.7264 (mmp80)
REVERT: C   21 MET cc_start: 0.8012 (mmm) cc_final: 0.7699 (tpp)
REVERT: F  135 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8100 (mp)
REVERT: F  177 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7502 (mp)
REVERT: F  292 ARG cc_start: 0.7611 (mpp80) cc_final: 0.6482 (mtm-85)
REVERT: D  272 ASP cc_start: 0.7264 (m-30) cc_final: 0.6974 (m-30)
  outliers start: 19
  outliers final: 11
  residues processed: 131
  average time/residue: 1.1352
  time to fit residues: 159.9413
Evaluate side-chains
  125 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ARG
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain E residue   85 SER
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain F residue  108 THR
Chi-restraints excluded: chain F residue  113 THR
Chi-restraints excluded: chain F residue  135 LEU
Chi-restraints excluded: chain F residue  177 LEU
Chi-restraints excluded: chain F residue  191 CYS
Chi-restraints excluded: chain F residue  309 ILE
Chi-restraints excluded: chain D residue   18 MET
Chi-restraints excluded: chain D residue  316 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 110 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   chunk 42 optimal weight:    0.4980
   chunk 33 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 76 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 63 optimal weight:    0.4980
   chunk 39 optimal weight:    0.0270
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  77 ASN
** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 255 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.136671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.106178 restraints weight = 20198.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.57
r_work: 0.3036 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2891
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2891 r_free = 0.2891    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2891 r_free = 0.2891    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2891
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.2046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   9103  Z= 0.109
  Angle     :  0.498   7.630  12321  Z= 0.262
  Chirality :  0.041   0.286   1410
  Planarity :  0.004   0.058   1539
  Dihedral  :  4.470  29.135   1243
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 17.50 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.25), residues: 1116
  helix:  2.65 (0.25), residues: 387
  sheet:  0.67 (0.31), residues: 272
  loop : -0.30 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 168 
 HIS   0.003   0.001   HIS A 141 
 PHE   0.012   0.001   PHE D 189 
 TYR   0.025   0.001   TYR E 235 
 ARG   0.011   0.000   ARG F 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03292 (  465)
  hydrogen bonds       : angle       4.07224 ( 1312)
  SS BOND              : bond        0.00245 (    4)
  SS BOND              : angle       1.25485 (    8)
  covalent geometry    : bond        0.00253 ( 9099)
  covalent geometry    : angle       0.49702 (12313)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 1.979 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7499 (mpt-90)
REVERT: A   45 ARG cc_start: 0.8069 (mtp85) cc_final: 0.7178 (mpt180)
REVERT: A  196 ARG cc_start: 0.7893 (mtt-85) cc_final: 0.7169 (mmp80)
REVERT: F  135 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7970 (mp)
REVERT: F  177 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7435 (mp)
REVERT: F  292 ARG cc_start: 0.7570 (mpp80) cc_final: 0.6418 (mtm-85)
REVERT: D  272 ASP cc_start: 0.7176 (m-30) cc_final: 0.6873 (m-30)
  outliers start: 18
  outliers final: 11
  residues processed: 130
  average time/residue: 1.8588
  time to fit residues: 260.8339
Evaluate side-chains
  126 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 2.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ARG
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain F residue  108 THR
Chi-restraints excluded: chain F residue  113 THR
Chi-restraints excluded: chain F residue  135 LEU
Chi-restraints excluded: chain F residue  177 LEU
Chi-restraints excluded: chain F residue  191 CYS
Chi-restraints excluded: chain F residue  309 ILE
Chi-restraints excluded: chain D residue   18 MET
Chi-restraints excluded: chain D residue  261 ASP
Chi-restraints excluded: chain D residue  316 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 110 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0570
   chunk 8 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   chunk 104 optimal weight:    5.9990
   chunk 102 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.6900

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

Flipped N/Q/H residues before XYZ refinement:
** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  77 ASN
** E 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 255 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.135475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.104636 restraints weight = 17600.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 2.41
r_work: 0.3036 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2906 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2891
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2891 r_free = 0.2891    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2891 r_free = 0.2891    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2891
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   9103  Z= 0.119
  Angle     :  0.514  10.492  12321  Z= 0.268
  Chirality :  0.041   0.302   1410
  Planarity :  0.004   0.060   1539
  Dihedral  :  4.500  29.128   1243
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 17.71 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.25), residues: 1116
  helix:  2.62 (0.25), residues: 387
  sheet:  0.69 (0.31), residues: 272
  loop : -0.31 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 168 
 HIS   0.003   0.001   HIS A 141 
 PHE   0.012   0.001   PHE D 189 
 TYR   0.026   0.001   TYR E 235 
 ARG   0.011   0.000   ARG F 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03349 (  465)
  hydrogen bonds       : angle       4.10025 ( 1312)
  SS BOND              : bond        0.00291 (    4)
  SS BOND              : angle       1.24345 (    8)
  covalent geometry    : bond        0.00279 ( 9099)
  covalent geometry    : angle       0.51316 (12313)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 1.107 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7489 (mpt-90)
REVERT: A   45 ARG cc_start: 0.8041 (mtp85) cc_final: 0.7153 (mpt180)
REVERT: A  196 ARG cc_start: 0.7879 (mtt-85) cc_final: 0.7172 (mmp80)
REVERT: F  119 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7095 (mp)
REVERT: F  177 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7421 (mp)
REVERT: F  292 ARG cc_start: 0.7625 (mpp80) cc_final: 0.6460 (mtm-85)
REVERT: D  272 ASP cc_start: 0.7161 (m-30) cc_final: 0.6847 (m-30)
  outliers start: 19
  outliers final: 12
  residues processed: 127
  average time/residue: 1.1447
  time to fit residues: 156.0007
Evaluate side-chains
  128 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ARG
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain F residue  108 THR
Chi-restraints excluded: chain F residue  113 THR
Chi-restraints excluded: chain F residue  119 LEU
Chi-restraints excluded: chain F residue  177 LEU
Chi-restraints excluded: chain F residue  191 CYS
Chi-restraints excluded: chain F residue  309 ILE
Chi-restraints excluded: chain D residue   18 MET
Chi-restraints excluded: chain D residue  261 ASP
Chi-restraints excluded: chain D residue  316 THR
Chi-restraints excluded: chain D residue  329 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 90 optimal weight:    0.8980
   chunk 96 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 104 optimal weight:    0.9980
   chunk 97 optimal weight:    0.8980
   chunk 64 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  77 ASN
E 171 ASN
D 255 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.134617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.105348 restraints weight = 24696.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3123 rms_B_bonded: 2.82
r_work: 0.2951 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2821 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2830
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2830 r_free = 0.2830    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2830 r_free = 0.2830    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2830
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   9103  Z= 0.137
  Angle     :  0.532   9.095  12321  Z= 0.277
  Chirality :  0.042   0.304   1410
  Planarity :  0.004   0.059   1539
  Dihedral  :  4.623  29.928   1243
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 17.71 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.25), residues: 1116
  helix:  2.57 (0.25), residues: 387
  sheet:  0.66 (0.31), residues: 277
  loop : -0.28 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E  47 
 HIS   0.004   0.001   HIS A 141 
 PHE   0.013   0.001   PHE D 189 
 TYR   0.029   0.001   TYR E 235 
 ARG   0.011   0.000   ARG F 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03482 (  465)
  hydrogen bonds       : angle       4.15862 ( 1312)
  SS BOND              : bond        0.00322 (    4)
  SS BOND              : angle       1.33720 (    8)
  covalent geometry    : bond        0.00325 ( 9099)
  covalent geometry    : angle       0.53129 (12313)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7830.22 seconds
wall clock time: 137 minutes 8.36 seconds (8228.36 seconds total)