Starting phenix.real_space_refine
on Tue Mar  3 21:48:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vig_32008/03_2026/7vig_32008.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vig_32008/03_2026/7vig_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_32008/03_2026/7vig_32008.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vig_32008/03_2026/7vig_32008.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vig_32008/03_2026/7vig_32008.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vig_32008/03_2026/7vig_32008.cif"
  }
  resolution = 2.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.051
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.21, per 1000 atoms: 0.25
  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: 0.70
  Conformation dependent library (CDL) restraints added in 381.9 milliseconds
  

  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: 0.32
  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: 1.44

  Time building geometry restraints manager: 0.91 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:             1.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.760
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.840
-------------------------------------------------------------------------------
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 : 8.30
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.005   0.000   ARG A 133 
 TYR   0.038   0.002   TYR E 235 
 PHE   0.014   0.001   PHE D 189 
 TRP   0.014   0.001   TRP A  81 
 HIS   0.006   0.001   HIS A 141 

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

*********************** 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  : 0.208 
Fit side-chains
REVERT: E   34 MET cc_start: 0.8934 (mmm) cc_final: 0.8671 (mmt)
REVERT: D  272 ASP cc_start: 0.7086 (m-30) cc_final: 0.6781 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.5884
  time to fit residues: 88.6644
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  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    0.0470
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    8.9990
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    2.2086

-------------------------------------------------------------------------------
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
F 156 ASN
** 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 = 0.3437 r_free = 0.3437 target = 0.128032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.098823 restraints weight = 19246.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 2.34
r_work: 0.2898 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2768 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2720
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2720 r_free = 0.2720    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2720 r_free = 0.2720    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2720
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.1268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   9103  Z= 0.262
  Angle     :  0.676   9.541  12321  Z= 0.344
  Chirality :  0.047   0.268   1410
  Planarity :  0.005   0.061   1539
  Dihedral  :  6.530  67.111   1243
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  :  8.90 %
    Favored  : 88.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.25), residues: 1116
  helix:  2.00 (0.25), residues: 386
  sheet:  0.50 (0.31), residues: 268
  loop : -0.57 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F 233 
 TYR   0.042   0.002   TYR E 235 
 PHE   0.013   0.002   PHE A 150 
 TRP   0.015   0.002   TRP E  47 
 HIS   0.008   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00617 ( 9099)
  covalent geometry    : angle       0.67477 (12313)
  SS BOND              : bond        0.00452 (    4)
  SS BOND              : angle       1.45950 (    8)
  hydrogen bonds       : bond        0.04596 (  465)
  hydrogen bonds       : angle       4.73637 ( 1312)

*********************** 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
  139 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.338 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7702 (mpt-90)
REVERT: A  216 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8347 (ppp)
REVERT: A  218 ARG cc_start: 0.8388 (mtp85) cc_final: 0.8188 (mtp85)
REVERT: C   47 GLU cc_start: 0.8282 (mp0) cc_final: 0.7721 (mp0)
REVERT: E  230 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8285 (ttt)
REVERT: D  272 ASP cc_start: 0.7271 (m-30) cc_final: 0.6731 (m-30)
  outliers start: 21
  outliers final: 10
  residues processed: 127
  average time/residue: 0.5596
  time to fit residues: 75.8550
Evaluate side-chains
  115 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
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  216 MET
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 D residue   18 MET
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain D residue  316 THR
Chi-restraints excluded: chain D residue  324 THR
Chi-restraints excluded: chain D residue  329 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 33 optimal weight:    9.9990
   chunk 62 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 101 optimal weight:    3.9990
   chunk 95 optimal weight:    0.0170
   chunk 46 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.7218

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

Flipped N/Q/H residues before XYZ refinement:
E  77 ASN
E 186 GLN
F 303 ASN
** 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 = 0.3504 r_free = 0.3504 target = 0.132678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.103519 restraints weight = 25502.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 2.90
r_work: 0.2973 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2831
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2831
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.1437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9103  Z= 0.128
  Angle     :  0.562   7.761  12321  Z= 0.288
  Chirality :  0.042   0.239   1410
  Planarity :  0.004   0.052   1539
  Dihedral  :  5.959  50.772   1243
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 12.59 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.25), residues: 1116
  helix:  2.21 (0.25), residues: 392
  sheet:  0.54 (0.30), residues: 268
  loop : -0.71 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F 233 
 TYR   0.035   0.001   TYR E 235 
 PHE   0.012   0.001   PHE D 189 
 TRP   0.013   0.001   TRP A 168 
 HIS   0.005   0.001   HIS F  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9099)
  covalent geometry    : angle       0.55961 (12313)
  SS BOND              : bond        0.00347 (    4)
  SS BOND              : angle       2.07087 (    8)
  hydrogen bonds       : bond        0.03683 (  465)
  hydrogen bonds       : angle       4.38508 ( 1312)

*********************** 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
  143 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A   45 ARG cc_start: 0.8095 (mtp85) cc_final: 0.7177 (mpt180)
REVERT: C   17 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6311 (mp0)
REVERT: C   47 GLU cc_start: 0.8214 (mp0) cc_final: 0.7630 (mp0)
REVERT: F   28 HIS cc_start: 0.7066 (m90) cc_final: 0.6756 (m170)
REVERT: F  292 ARG cc_start: 0.7512 (mpp80) cc_final: 0.6488 (mtt90)
REVERT: D  272 ASP cc_start: 0.7198 (m-30) cc_final: 0.6863 (m-30)
  outliers start: 18
  outliers final: 8
  residues processed: 132
  average time/residue: 0.5319
  time to fit residues: 75.1487
Evaluate side-chains
  118 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  261 MET
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain C residue   17 GLU
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  164 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 27 optimal weight:    0.0970
   chunk 39 optimal weight:    9.9990
   chunk 60 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 76 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   chunk 108 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 72 optimal weight:    6.9990
   chunk 44 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.6778

-------------------------------------------------------------------------------
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
D 255 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.134237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.104702 restraints weight = 28270.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 3.19
r_work: 0.2993 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2956
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2956 r_free = 0.2956    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2956 r_free = 0.2956    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2956
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9103  Z= 0.117
  Angle     :  0.515   7.326  12321  Z= 0.270
  Chirality :  0.041   0.220   1410
  Planarity :  0.004   0.057   1539
  Dihedral  :  5.194  39.662   1243
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 13.51 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.17 (0.25), residues: 1116
  helix:  2.48 (0.25), residues: 387
  sheet:  0.58 (0.31), residues: 260
  loop : -0.56 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F 233 
 TYR   0.037   0.001   TYR E 235 
 PHE   0.013   0.001   PHE D 189 
 TRP   0.012   0.001   TRP A 168 
 HIS   0.004   0.001   HIS F  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9099)
  covalent geometry    : angle       0.51294 (12313)
  SS BOND              : bond        0.00347 (    4)
  SS BOND              : angle       1.71753 (    8)
  hydrogen bonds       : bond        0.03456 (  465)
  hydrogen bonds       : angle       4.16313 ( 1312)

*********************** 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
  139 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7472 (mpt-90)
REVERT: A   45 ARG cc_start: 0.7866 (mtp85) cc_final: 0.7007 (mpt180)
REVERT: C   21 MET cc_start: 0.7855 (mmm) cc_final: 0.7637 (tpp)
REVERT: F   28 HIS cc_start: 0.7192 (m90) cc_final: 0.6784 (m170)
REVERT: F  135 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7739 (mp)
REVERT: F  292 ARG cc_start: 0.7476 (mpp80) cc_final: 0.6439 (mtt90)
REVERT: F  302 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7200 (mp)
REVERT: D  272 ASP cc_start: 0.6949 (m-30) cc_final: 0.6654 (m-30)
  outliers start: 23
  outliers final: 10
  residues processed: 128
  average time/residue: 0.5350
  time to fit residues: 73.2422
Evaluate side-chains
  117 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
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  164 ILE
Chi-restraints excluded: chain F residue  171 SER
Chi-restraints excluded: chain F residue  213 LEU
Chi-restraints excluded: chain F residue  302 LEU
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 13 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 95 optimal weight:    1.9990
   chunk 109 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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
F  86 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.133594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.104539 restraints weight = 30778.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 3.46
r_work: 0.2972 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2972
-------------------------------------------------------------------------------
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 = 0.47   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 = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2946
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9103  Z= 0.130
  Angle     :  0.513   7.476  12321  Z= 0.272
  Chirality :  0.041   0.226   1410
  Planarity :  0.004   0.057   1539
  Dihedral  :  5.013  36.886   1243
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 14.84 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.25), residues: 1116
  helix:  2.37 (0.25), residues: 393
  sheet:  0.62 (0.31), residues: 262
  loop : -0.62 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F 233 
 TYR   0.037   0.001   TYR E 235 
 PHE   0.012   0.001   PHE D 189 
 TRP   0.011   0.001   TRP A 168 
 HIS   0.004   0.001   HIS F  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9099)
  covalent geometry    : angle       0.51183 (12313)
  SS BOND              : bond        0.00396 (    4)
  SS BOND              : angle       1.61659 (    8)
  hydrogen bonds       : bond        0.03499 (  465)
  hydrogen bonds       : angle       4.16356 ( 1312)

*********************** 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
  134 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7497 (mpt-90)
REVERT: A   45 ARG cc_start: 0.7886 (mtp85) cc_final: 0.7032 (mpt180)
REVERT: A  213 ARG cc_start: 0.8703 (mmm-85) cc_final: 0.8146 (mmt90)
REVERT: F  135 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7741 (mp)
REVERT: F  292 ARG cc_start: 0.7501 (mpp80) cc_final: 0.6454 (mtt90)
REVERT: F  302 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7177 (mp)
REVERT: D  272 ASP cc_start: 0.6942 (m-30) cc_final: 0.6639 (m-30)
  outliers start: 23
  outliers final: 12
  residues processed: 123
  average time/residue: 0.5432
  time to fit residues: 71.5738
Evaluate side-chains
  117 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
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  227 ASP
Chi-restraints excluded: chain E residue    3 GLN
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  171 SER
Chi-restraints excluded: chain F residue  213 LEU
Chi-restraints excluded: chain F residue  302 LEU
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 68 optimal weight:    2.9990
   chunk 66 optimal weight:    6.9990
   chunk 6 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 76 optimal weight:    7.9990
   chunk 105 optimal weight:    6.9990
   chunk 109 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    1.7588

-------------------------------------------------------------------------------
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
D 255 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.130836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.100800 restraints weight = 14379.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 2.12
r_work: 0.2980 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2854
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2854
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9103  Z= 0.213
  Angle     :  0.578   6.929  12321  Z= 0.307
  Chirality :  0.044   0.235   1410
  Planarity :  0.004   0.057   1539
  Dihedral  :  5.510  37.274   1243
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 14.84 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.25), residues: 1116
  helix:  2.28 (0.25), residues: 387
  sheet:  0.42 (0.31), residues: 286
  loop : -0.64 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F 233 
 TYR   0.029   0.002   TYR E 235 
 PHE   0.013   0.002   PHE D 189 
 TRP   0.013   0.001   TRP E  47 
 HIS   0.006   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 ( 9099)
  covalent geometry    : angle       0.57559 (12313)
  SS BOND              : bond        0.00623 (    4)
  SS BOND              : angle       2.17704 (    8)
  hydrogen bonds       : bond        0.04067 (  465)
  hydrogen bonds       : angle       4.38484 ( 1312)

*********************** 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
  135 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7584 (mpt-90)
REVERT: A   45 ARG cc_start: 0.8028 (mtp85) cc_final: 0.7159 (mpt180)
REVERT: C   17 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.6247 (mp0)
REVERT: C   21 MET cc_start: 0.7975 (mmm) cc_final: 0.7666 (tpp)
REVERT: E  160 ARG cc_start: 0.7604 (ttp-170) cc_final: 0.7332 (mtm110)
REVERT: E  235 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.7540 (t80)
REVERT: F  135 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7911 (mp)
REVERT: F  274 ILE cc_start: 0.7841 (mt) cc_final: 0.7597 (mp)
REVERT: F  302 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7231 (mp)
REVERT: D   53 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7832 (mpt)
REVERT: D  272 ASP cc_start: 0.7081 (m-30) cc_final: 0.6554 (m-30)
  outliers start: 28
  outliers final: 11
  residues processed: 123
  average time/residue: 0.5720
  time to fit residues: 75.0855
Evaluate side-chains
  118 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ARG
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain C residue   17 GLU
Chi-restraints excluded: chain E residue    3 GLN
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 E residue  235 TYR
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  302 LEU
Chi-restraints excluded: chain F residue  309 ILE
Chi-restraints excluded: chain D residue   18 MET
Chi-restraints excluded: chain D residue   53 MET
Chi-restraints excluded: chain D residue  316 THR
Chi-restraints excluded: chain D residue  324 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9990
   chunk 50 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0980
   chunk 105 optimal weight:    4.9990
   chunk 37 optimal weight:    0.4980
   overall best weight:    0.6984

-------------------------------------------------------------------------------
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 179 GLN
D 255 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.133570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.103335 restraints weight = 17929.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 2.43
r_work: 0.3024 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
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 = 0.47   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 = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2888
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9103  Z= 0.118
  Angle     :  0.508   7.728  12321  Z= 0.269
  Chirality :  0.041   0.184   1410
  Planarity :  0.004   0.056   1539
  Dihedral  :  4.982  33.203   1243
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.76 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.25), residues: 1116
  helix:  2.45 (0.25), residues: 387
  sheet:  0.62 (0.31), residues: 279
  loop : -0.64 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG F 233 
 TYR   0.028   0.001   TYR E 235 
 PHE   0.012   0.001   PHE D 189 
 TRP   0.014   0.001   TRP A 168 
 HIS   0.003   0.001   HIS F  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 9099)
  covalent geometry    : angle       0.50689 (12313)
  SS BOND              : bond        0.00346 (    4)
  SS BOND              : angle       1.39270 (    8)
  hydrogen bonds       : bond        0.03447 (  465)
  hydrogen bonds       : angle       4.17737 ( 1312)

*********************** 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
  133 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7582 (mpt-90)
REVERT: A   45 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7251 (mpt180)
REVERT: A  213 ARG cc_start: 0.8742 (mmm-85) cc_final: 0.8123 (mmt90)
REVERT: C   20 LYS cc_start: 0.8165 (ttmm) cc_final: 0.7827 (mtpp)
REVERT: C   21 MET cc_start: 0.7936 (mmm) cc_final: 0.7575 (tpp)
REVERT: E  235 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.7221 (t80)
REVERT: F  135 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7992 (mp)
REVERT: F  274 ILE cc_start: 0.7877 (mt) cc_final: 0.7628 (mp)
REVERT: F  302 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7312 (mp)
REVERT: D   53 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7892 (mpt)
REVERT: D  272 ASP cc_start: 0.7203 (m-30) cc_final: 0.6892 (m-30)
  outliers start: 24
  outliers final: 11
  residues processed: 125
  average time/residue: 0.5225
  time to fit residues: 69.9979
Evaluate side-chains
  118 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
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    3 GLN
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  147 VAL
Chi-restraints excluded: chain E residue  235 TYR
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  207 THR
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   53 MET
Chi-restraints excluded: chain D residue  316 THR
Chi-restraints excluded: chain D residue  324 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 72 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 96 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 42 optimal weight:    0.4980
   chunk 81 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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
D 255 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.134227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.105432 restraints weight = 21321.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 2.48
r_work: 0.2988 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2858 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2849
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2849 r_free = 0.2849    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2849 r_free = 0.2849    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2849
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9103  Z= 0.114
  Angle     :  0.502   6.911  12321  Z= 0.266
  Chirality :  0.041   0.170   1410
  Planarity :  0.004   0.059   1539
  Dihedral  :  4.819  31.287   1243
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.66 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.25), residues: 1116
  helix:  2.55 (0.25), residues: 387
  sheet:  0.65 (0.32), residues: 264
  loop : -0.55 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG F 233 
 TYR   0.027   0.001   TYR E 235 
 PHE   0.012   0.001   PHE D 189 
 TRP   0.013   0.001   TRP A 168 
 HIS   0.005   0.001   HIS F  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 9099)
  covalent geometry    : angle       0.50028 (12313)
  SS BOND              : bond        0.00318 (    4)
  SS BOND              : angle       1.62745 (    8)
  hydrogen bonds       : bond        0.03414 (  465)
  hydrogen bonds       : angle       4.12856 ( 1312)

*********************** 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
  134 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 109
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7580 (mpt-90)
REVERT: A   45 ARG cc_start: 0.8121 (mtp85) cc_final: 0.7241 (mpt180)
REVERT: A  213 ARG cc_start: 0.8778 (mmm-85) cc_final: 0.8143 (mmt90)
REVERT: E  235 TYR cc_start: 0.7507 (OUTLIER) cc_final: 0.7239 (t80)
REVERT: F  135 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7998 (mp)
REVERT: F  274 ILE cc_start: 0.7839 (mt) cc_final: 0.7580 (mp)
REVERT: D   53 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7828 (mpt)
REVERT: D  272 ASP cc_start: 0.7173 (m-30) cc_final: 0.6859 (m-30)
  outliers start: 25
  outliers final: 12
  residues processed: 124
  average time/residue: 0.5340
  time to fit residues: 70.9248
Evaluate side-chains
  121 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
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  227 ASP
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 E residue  235 TYR
Chi-restraints excluded: chain F residue   28 HIS
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  207 THR
Chi-restraints excluded: chain F residue  309 ILE
Chi-restraints excluded: chain D residue   18 MET
Chi-restraints excluded: chain D residue   53 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 60 optimal weight:    0.0970
   chunk 82 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 103 optimal weight:    0.7980
   chunk 88 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 108 optimal weight:    0.0980
   chunk 63 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 105 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  77 ASN
D 241 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 = 0.3535 r_free = 0.3535 target = 0.135458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.105175 restraints weight = 29870.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 3.44
r_work: 0.2971 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2971
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2971 r_free = 0.2971    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2971 r_free = 0.2971    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2971
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.2058

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= 0.106
  Angle     :  0.495   7.386  12321  Z= 0.260
  Chirality :  0.040   0.159   1410
  Planarity :  0.004   0.057   1539
  Dihedral  :  4.614  28.647   1243
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.48 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.25), residues: 1116
  helix:  2.63 (0.25), residues: 387
  sheet:  0.69 (0.32), residues: 264
  loop : -0.48 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG F 233 
 TYR   0.027   0.001   TYR E 235 
 PHE   0.011   0.001   PHE D 189 
 TRP   0.013   0.001   TRP A 168 
 HIS   0.003   0.001   HIS F  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 9099)
  covalent geometry    : angle       0.49376 (12313)
  SS BOND              : bond        0.00291 (    4)
  SS BOND              : angle       1.60764 (    8)
  hydrogen bonds       : bond        0.03307 (  465)
  hydrogen bonds       : angle       4.05383 ( 1312)

*********************** 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
  141 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7478 (mpt-90)
REVERT: A   45 ARG cc_start: 0.7966 (mtp85) cc_final: 0.7119 (mpt180)
REVERT: A  213 ARG cc_start: 0.8731 (mmm-85) cc_final: 0.8177 (mmt90)
REVERT: C   20 LYS cc_start: 0.8087 (ttmm) cc_final: 0.7762 (mtpp)
REVERT: E  235 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.6930 (t80)
REVERT: F  135 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7794 (mp)
REVERT: D   18 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8148 (ttt)
REVERT: D  272 ASP cc_start: 0.7031 (m-30) cc_final: 0.6722 (m-30)
  outliers start: 21
  outliers final: 11
  residues processed: 133
  average time/residue: 0.5519
  time to fit residues: 78.4206
Evaluate side-chains
  122 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
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 A residue  227 ASP
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 E residue  235 TYR
Chi-restraints excluded: chain F residue   28 HIS
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  309 ILE
Chi-restraints excluded: chain D residue   18 MET
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 1 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 45 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9980
   chunk 27 optimal weight:    0.4980
   chunk 9 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   chunk 56 optimal weight:    0.4980
   chunk 62 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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
D 241 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 = 0.3531 r_free = 0.3531 target = 0.135172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.104099 restraints weight = 18761.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 2.48
r_work: 0.3018 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2889 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2884
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2884
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9103  Z= 0.116
  Angle     :  0.513  10.302  12321  Z= 0.267
  Chirality :  0.041   0.161   1410
  Planarity :  0.004   0.059   1539
  Dihedral  :  4.615  28.547   1243
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 17.20 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.25), residues: 1116
  helix:  2.66 (0.25), residues: 387
  sheet:  0.67 (0.32), residues: 269
  loop : -0.43 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG F 233 
 TYR   0.027   0.001   TYR E 235 
 PHE   0.011   0.001   PHE D 189 
 TRP   0.012   0.001   TRP A 168 
 HIS   0.003   0.001   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9099)
  covalent geometry    : angle       0.51121 (12313)
  SS BOND              : bond        0.00327 (    4)
  SS BOND              : angle       1.61871 (    8)
  hydrogen bonds       : bond        0.03385 (  465)
  hydrogen bonds       : angle       4.06790 ( 1312)

********************** 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
  129 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7543 (mpt-90)
REVERT: A   45 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7181 (mpt180)
REVERT: A  213 ARG cc_start: 0.8774 (mmm-85) cc_final: 0.8211 (mmt90)
REVERT: C   20 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7772 (mtpp)
REVERT: C   21 MET cc_start: 0.7931 (mmm) cc_final: 0.7493 (tpp)
REVERT: E  235 TYR cc_start: 0.7323 (OUTLIER) cc_final: 0.7049 (t80)
REVERT: D  272 ASP cc_start: 0.7121 (m-30) cc_final: 0.6814 (m-30)
  outliers start: 18
  outliers final: 12
  residues processed: 125
  average time/residue: 0.5674
  time to fit residues: 75.6712
Evaluate side-chains
  121 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
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  233 PHE
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 E residue  235 TYR
Chi-restraints excluded: chain F residue   28 HIS
Chi-restraints excluded: chain F residue  108 THR
Chi-restraints excluded: chain F residue  113 THR
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  324 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A  74 GLN
** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  77 ASN
D 241 ASN
D 255 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.133649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.104642 restraints weight = 21484.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 2.52
r_work: 0.2959 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2826 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2829
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2829
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9103  Z= 0.138
  Angle     :  0.526   9.640  12321  Z= 0.275
  Chirality :  0.041   0.176   1410
  Planarity :  0.004   0.057   1539
  Dihedral  :  4.811  30.516   1243
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.89 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.25), residues: 1116
  helix:  2.61 (0.25), residues: 387
  sheet:  0.66 (0.32), residues: 268
  loop : -0.43 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG F 233 
 TYR   0.029   0.001   TYR E 235 
 PHE   0.012   0.001   PHE D 189 
 TRP   0.011   0.001   TRP E  47 
 HIS   0.005   0.001   HIS F  28 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 9099)
  covalent geometry    : angle       0.52423 (12313)
  SS BOND              : bond        0.00442 (    4)
  SS BOND              : angle       1.92881 (    8)
  hydrogen bonds       : bond        0.03548 (  465)
  hydrogen bonds       : angle       4.12834 ( 1312)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3404.97 seconds
wall clock time: 58 minutes 45.04 seconds (3525.04 seconds total)