Starting phenix.real_space_refine
on Wed Mar 12 04:38:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jlo_36402/03_2025/8jlo_36402.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jlo_36402/03_2025/8jlo_36402.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jlo_36402/03_2025/8jlo_36402.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jlo_36402/03_2025/8jlo_36402.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jlo_36402/03_2025/8jlo_36402.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jlo_36402/03_2025/8jlo_36402.cif"
  }
  resolution = 3.52
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.031
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      59      5.16       5
     C    4690      2.51       5
     N    1266      2.21       5
     O    1328      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7343
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 240, 1972
          Classifications: {'peptide': 240}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 6, 'TRANS': 233}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "B"
      Number of atoms: 2593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2593
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "R"
      Number of atoms: 2321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2321
          Classifications: {'peptide': 286}
          Link IDs: {'PTRANS': 11, 'TRANS': 274}
          Chain breaks: 1
    Chain: "Y"
      Number of atoms: 445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 445
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "R"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Unusual residues: {'UJL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.93, per 1000 atoms: 0.67
  Number of scatterers: 7343
  At special positions: 0
  Unit cell: (74.8, 102.85, 131.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      59     16.00
     O    1328      8.00
     N    1266      7.00
     C    4690      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 182 " 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: 1.83
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1748

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 8 sheets defined
      46.3% alpha, 14.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 38
      removed outlier: 3.505A  pdb=" N   ALA A  18 " --> pdb=" O   ASN A  14 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
    Processing helix  chain 'A' and resid 232 through 237
      removed outlier: 3.794A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.184A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 317
      removed outlier: 3.772A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.879A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ARG A 336 " --> pdb=" O   PRO A 332 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   ALA A 337 " --> pdb=" O   ARG A 333 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ARG A 342 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASP A 343 " --> pdb=" O   TYR A 339 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   GLU A 344 " --> pdb=" O   PHE A 340 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.564A  pdb=" N   GLN A 390 " --> pdb=" O   MET A 386 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   TYR A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
      removed outlier: 3.658A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'R' and resid 22 through 51
      removed outlier: 3.647A  pdb=" N   PHE R  51 " --> pdb=" O   SER R  47 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 56 through 76
      removed outlier: 3.592A  pdb=" N   TRP R  60 " --> pdb=" O   THR R  56 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   VAL R  76 " --> pdb=" O   LEU R  72 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 76 through 87
    Processing helix  chain 'R' and resid 92 through 125
      removed outlier: 3.808A  pdb=" N   SER R 110 " --> pdb=" O   LEU R 106 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 136 through 161
      removed outlier: 3.715A  pdb=" N   VAL R 150 " --> pdb=" O   ILE R 146 " (cutoff:3.500A)
      Proline residue:  R 151  - end of helix
    Processing helix  chain 'R' and resid 169 through 176
    Processing helix  chain 'R' and resid 187 through 199
      removed outlier: 4.024A  pdb=" N   VAL R 192 " --> pdb=" O   LYS R 188 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 199 through 233
      removed outlier: 3.888A  pdb=" N   ILE R 233 " --> pdb=" O   GLN R 229 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 248 through 277
      removed outlier: 3.953A  pdb=" N   ILE R 255 " --> pdb=" O   LYS R 251 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   VAL R 256 " --> pdb=" O   THR R 252 " (cutoff:3.500A)
      Proline residue:  R 266  - end of helix
      Proline residue:  R 275  - end of helix
    Processing helix  chain 'R' and resid 282 through 299
      removed outlier: 3.818A  pdb=" N   ASN R 286 " --> pdb=" O   PRO R 282 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   VAL R 288 " --> pdb=" O   THR R 284 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLY R 293 " --> pdb=" O   LEU R 289 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   TYR R 294 " --> pdb=" O   ILE R 290 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 308 through 319
      removed outlier: 3.690A  pdb=" N   ARG R 312 " --> pdb=" O   TYR R 308 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 7 through 24
    Processing helix  chain 'Y' and resid 29 through 44
      removed outlier: 3.564A  pdb=" N   ALA Y  33 " --> pdb=" O   LYS Y  29 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   HIS Y  44 " --> pdb=" O   TYR Y  40 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214
      removed outlier: 10.223A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.120A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.024A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.635A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.431A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51
      removed outlier: 3.764A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ALA B 328 " --> pdb=" O   GLY B 319 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63
      removed outlier: 3.988A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 5.354A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 5.100A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105
      removed outlier: 3.647A  pdb=" N   SER B 122 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 5.898A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.491A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.585A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.406A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.958A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   CYS B 250 " --> pdb=" O   TYR B 264 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LEU B 252 " --> pdb=" O   MET B 262 " (cutoff:3.500A)
      removed outlier: 4.739A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278

    361 hydrogen bonds defined for protein.
    1050 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.02

  Time building geometry restraints manager: 2.14 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2362
        1.34 -     1.46: 1549
        1.46 -     1.58: 3505
        1.58 -     1.69: 0
        1.69 -     1.81: 88
  Bond restraints: 7504
  Sorted by residual:
  bond pdb=" C   THR B  29 "
       pdb=" O   THR B  29 "
    ideal  model  delta    sigma   weight residual
    1.234  1.285 -0.051 1.26e-02 6.30e+03 1.62e+01
  bond pdb=" N   THR B  34 "
       pdb=" CA  THR B  34 "
    ideal  model  delta    sigma   weight residual
    1.456  1.499 -0.043 1.32e-02 5.74e+03 1.08e+01
  bond pdb=" N   ILE B  33 "
       pdb=" CA  ILE B  33 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.037 1.26e-02 6.30e+03 8.78e+00
  bond pdb=" CA  SER R  80 "
       pdb=" CB  SER R  80 "
    ideal  model  delta    sigma   weight residual
    1.529  1.483  0.046 1.55e-02 4.16e+03 8.68e+00
  bond pdb=" N   THR B  29 "
       pdb=" CA  THR B  29 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.036 1.27e-02 6.20e+03 7.98e+00
  ... (remaining 7499 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 9921
        2.05 -     4.09: 207
        4.09 -     6.14: 22
        6.14 -     8.18: 1
        8.18 -    10.23: 3
  Bond angle restraints: 10154
  Sorted by residual:
  angle pdb=" N   GLU B 172 "
        pdb=" CA  GLU B 172 "
        pdb=" C   GLU B 172 "
      ideal   model   delta    sigma   weight residual
     114.75  108.11    6.64 1.26e+00 6.30e-01 2.77e+01
  angle pdb=" CB  ARG B  19 "
        pdb=" CG  ARG B  19 "
        pdb=" CD  ARG B  19 "
      ideal   model   delta    sigma   weight residual
     111.30  121.53  -10.23 2.30e+00 1.89e-01 1.98e+01
  angle pdb=" N   ILE B 171 "
        pdb=" CA  ILE B 171 "
        pdb=" C   ILE B 171 "
      ideal   model   delta    sigma   weight residual
     106.21  110.52   -4.31 1.07e+00 8.73e-01 1.62e+01
  angle pdb=" N   TYR R 294 "
        pdb=" CA  TYR R 294 "
        pdb=" C   TYR R 294 "
      ideal   model   delta    sigma   weight residual
     111.07  106.90    4.17 1.07e+00 8.73e-01 1.52e+01
  angle pdb=" N   SER R  80 "
        pdb=" CA  SER R  80 "
        pdb=" C   SER R  80 "
      ideal   model   delta    sigma   weight residual
     111.07  106.96    4.11 1.07e+00 8.73e-01 1.48e+01
  ... (remaining 10149 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 4027
       17.73 -    35.46: 352
       35.46 -    53.19: 71
       53.19 -    70.93: 19
       70.93 -    88.66: 6
  Dihedral angle restraints: 4475
    sinusoidal: 1778
      harmonic: 2697
  Sorted by residual:
  dihedral pdb=" CA  LEU R  75 "
           pdb=" C   LEU R  75 "
           pdb=" N   VAL R  76 "
           pdb=" CA  VAL R  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.99  -19.01     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  ARG A 231 "
           pdb=" C   ARG A 231 "
           pdb=" N   ARG A 232 "
           pdb=" CA  ARG A 232 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.37   18.63     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  ILE B 171 "
           pdb=" C   ILE B 171 "
           pdb=" N   GLU B 172 "
           pdb=" CA  GLU B 172 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.62   18.38     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 4472 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 848
       0.045 -    0.091: 246
       0.091 -    0.136: 43
       0.136 -    0.182: 1
       0.182 -    0.227: 1
  Chirality restraints: 1139
  Sorted by residual:
  chirality pdb=" CA  MET R  77 "
            pdb=" N   MET R  77 "
            pdb=" C   MET R  77 "
            pdb=" CB  MET R  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CB  ILE B 338 "
            pdb=" CA  ILE B 338 "
            pdb=" CG1 ILE B 338 "
            pdb=" CG2 ILE B 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 5.02e-01
  chirality pdb=" CA  ILE B 232 "
            pdb=" N   ILE B 232 "
            pdb=" C   ILE B 232 "
            pdb=" CB  ILE B 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.46e-01
  ... (remaining 1136 not shown)

  Planarity restraints: 1282
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B  28 "   -0.018 2.00e-02 2.50e+03   3.63e-02 1.32e+01
        pdb=" C   ALA B  28 "    0.063 2.00e-02 2.50e+03
        pdb=" O   ALA B  28 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   THR B  29 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 220 "    0.011 2.00e-02 2.50e+03   1.63e-02 3.97e+00
        pdb=" CG  HIS A 220 "   -0.034 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 220 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 220 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 220 "    0.000 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 220 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  99 "    0.018 2.00e-02 2.50e+03   1.25e-02 3.92e+00
        pdb=" CG  TRP B  99 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  99 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  99 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  99 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  99 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  99 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  99 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  99 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  99 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1279 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1628
        2.79 -     3.31: 7023
        3.31 -     3.84: 11160
        3.84 -     4.37: 12677
        4.37 -     4.90: 22564
  Nonbonded interactions: 55052
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASN B 110 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OD1 ASP A 274 "
            pdb=" ND2 ASN A 278 "
     model   vdw
     2.336 3.120
  nonbonded pdb=" O   GLN B  75 "
            pdb=" OG  SER B  98 "
     model   vdw
     2.348 3.040
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.356 3.040
  nonbonded pdb=" O   ASP B 333 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.365 3.040
  ... (remaining 55047 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.760
  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:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.810
  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:3.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
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      :  0.003   0.051   7504  Z= 0.210
  Angle     :  0.690  10.227  10154  Z= 0.423
  Chirality :  0.042   0.227   1139
  Planarity :  0.004   0.037   1282
  Dihedral  : 14.264  88.658   2724
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  0.75 %
    Favored  : 98.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.28), residues: 910
  helix:  1.96 (0.26), residues: 394
  sheet: -2.04 (0.42), residues: 162
  loop : -2.47 (0.28), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP B  99 
 HIS   0.021   0.001   HIS A 220 
 PHE   0.020   0.001   PHE A 315 
 TYR   0.016   0.001   TYR A 253 
 ARG   0.018   0.001   ARG B  19 

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 132
  time to evaluate  : 0.814 
Fit side-chains
REVERT: A  215 ASP cc_start: 0.7936 (t70) cc_final: 0.7588 (t0)
REVERT: B   29 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7911 (p)
REVERT: B  325 MET cc_start: 0.8455 (mtt) cc_final: 0.8169 (mtm)
REVERT: R  162 GLU cc_start: 0.8875 (pt0) cc_final: 0.8674 (pm20)
REVERT: R  302 MET cc_start: 0.8018 (mtm) cc_final: 0.7401 (tmm)
  outliers start: 2
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1729
  time to fit residues: 31.8746
Evaluate side-chains
  114 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9980
   chunk 27 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   chunk 81 optimal weight:    0.0980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.187648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.145300 restraints weight = 9058.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.143321 restraints weight = 7143.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.145142 restraints weight = 8168.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.1155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7504  Z= 0.199
  Angle     :  0.588   9.191  10154  Z= 0.311
  Chirality :  0.042   0.171   1139
  Planarity :  0.004   0.047   1282
  Dihedral  :  4.454  41.509   1018
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 10.05 %
    Favored  : 88.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.28), residues: 910
  helix:  2.15 (0.26), residues: 395
  sheet: -1.79 (0.41), residues: 160
  loop : -2.23 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.015   0.001   HIS A 220 
 PHE   0.026   0.002   PHE R 165 
 TYR   0.012   0.001   TYR B 264 
 ARG   0.003   0.000   ARG A 389 

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.856 
Fit side-chains
REVERT: A  252 SER cc_start: 0.9251 (t) cc_final: 0.9016 (p)
REVERT: B   36 ASN cc_start: 0.8606 (p0) cc_final: 0.8341 (p0)
REVERT: B  325 MET cc_start: 0.8274 (mtt) cc_final: 0.8064 (mtm)
REVERT: R   27 TYR cc_start: 0.8594 (m-80) cc_final: 0.8253 (m-80)
  outliers start: 9
  outliers final: 7
  residues processed: 127
  average time/residue: 0.1689
  time to fit residues: 29.9144
Evaluate side-chains
  111 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain R residue  295 LEU
Chi-restraints excluded: chain R residue  303 VAL
Chi-restraints excluded: chain Y residue   42 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 89 optimal weight:    0.0670
   chunk 4 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 76 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   chunk 15 optimal weight:   10.0000
   chunk 44 optimal weight:    0.0000
   chunk 2 optimal weight:    0.0770
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.3280

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 264 ASN
A 294 GLN
B 259 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.190100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.148747 restraints weight = 8875.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.146522 restraints weight = 7095.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.148486 restraints weight = 7823.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.062   7504  Z= 0.146
  Angle     :  0.540  10.439  10154  Z= 0.281
  Chirality :  0.041   0.151   1139
  Planarity :  0.004   0.038   1282
  Dihedral  :  4.186  34.160   1018
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 12.94 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.29), residues: 910
  helix:  2.35 (0.26), residues: 396
  sheet: -1.62 (0.41), residues: 160
  loop : -2.10 (0.30), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.013   0.001   HIS A 220 
 PHE   0.025   0.001   PHE R 165 
 TYR   0.009   0.001   TYR A 311 
 ARG   0.007   0.000   ARG B  19 

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
REVERT: A  252 SER cc_start: 0.9218 (t) cc_final: 0.8995 (p)
REVERT: A  343 ASP cc_start: 0.7398 (m-30) cc_final: 0.6909 (m-30)
REVERT: B   36 ASN cc_start: 0.8564 (p0) cc_final: 0.8274 (p0)
REVERT: B  175 GLN cc_start: 0.8531 (mt0) cc_final: 0.8151 (mm-40)
REVERT: R   27 TYR cc_start: 0.8472 (m-80) cc_final: 0.8271 (m-80)
REVERT: R  196 MET cc_start: 0.8974 (mmt) cc_final: 0.8735 (mmm)
REVERT: R  302 MET cc_start: 0.6849 (tmm) cc_final: 0.6519 (tmm)
  outliers start: 8
  outliers final: 5
  residues processed: 121
  average time/residue: 0.1878
  time to fit residues: 30.9821
Evaluate side-chains
  107 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain Y residue   42 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0010
   chunk 11 optimal weight:    5.9990
   chunk 17 optimal weight:    6.9990
   chunk 63 optimal weight:    7.9990
   chunk 88 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 24 optimal weight:   10.0000
   chunk 78 optimal weight:    2.9990
   overall best weight:    1.1390

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.183111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.124159 restraints weight = 9126.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.128984 restraints weight = 5556.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.132088 restraints weight = 4240.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.1767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7504  Z= 0.204
  Angle     :  0.557  12.790  10154  Z= 0.291
  Chirality :  0.042   0.155   1139
  Planarity :  0.003   0.038   1282
  Dihedral  :  4.023  33.080   1017
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 13.07 %
    Favored  : 84.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.28), residues: 910
  helix:  2.09 (0.25), residues: 404
  sheet: -1.60 (0.40), residues: 164
  loop : -2.09 (0.31), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 339 
 HIS   0.010   0.001   HIS A 220 
 PHE   0.031   0.002   PHE R 154 
 TYR   0.019   0.001   TYR A 253 
 ARG   0.007   0.000   ARG B  19 

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.951 
Fit side-chains
REVERT: A  252 SER cc_start: 0.9188 (t) cc_final: 0.8937 (p)
REVERT: A  317 ARG cc_start: 0.8719 (mpp80) cc_final: 0.7613 (mpp-170)
REVERT: B  175 GLN cc_start: 0.8534 (mt0) cc_final: 0.7974 (mm-40)
REVERT: R   27 TYR cc_start: 0.8856 (m-80) cc_final: 0.8393 (m-80)
REVERT: R   86 GLU cc_start: 0.7004 (mp0) cc_final: 0.6801 (mp0)
REVERT: R  196 MET cc_start: 0.8889 (mmt) cc_final: 0.8607 (mmm)
REVERT: R  302 MET cc_start: 0.6855 (tmm) cc_final: 0.6570 (tmm)
  outliers start: 16
  outliers final: 10
  residues processed: 121
  average time/residue: 0.1905
  time to fit residues: 31.8254
Evaluate side-chains
  117 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain R residue  149 SER
Chi-restraints excluded: chain R residue  295 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 73 optimal weight:    0.0370
   chunk 43 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 54 optimal weight:    8.9990
   chunk 64 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.2064

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  36 ASN
R 286 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.185152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.143476 restraints weight = 9097.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.143367 restraints weight = 9027.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.144423 restraints weight = 9303.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   7504  Z= 0.202
  Angle     :  0.549  11.321  10154  Z= 0.289
  Chirality :  0.042   0.165   1139
  Planarity :  0.003   0.038   1282
  Dihedral  :  4.020  32.854   1017
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 15.08 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.28), residues: 910
  helix:  2.11 (0.25), residues: 404
  sheet: -1.56 (0.40), residues: 166
  loop : -2.00 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.009   0.001   HIS A 220 
 PHE   0.031   0.001   PHE R 165 
 TYR   0.019   0.001   TYR A 253 
 ARG   0.002   0.000   ARG B  19 

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 1.143 
Fit side-chains
REVERT: A  252 SER cc_start: 0.9182 (t) cc_final: 0.8961 (p)
REVERT: A  317 ARG cc_start: 0.8615 (mpp80) cc_final: 0.7622 (mpp-170)
REVERT: B   75 GLN cc_start: 0.8063 (mm110) cc_final: 0.7566 (mt0)
REVERT: R   27 TYR cc_start: 0.8634 (m-80) cc_final: 0.8192 (m-80)
REVERT: R  302 MET cc_start: 0.6927 (tmm) cc_final: 0.6698 (tmm)
  outliers start: 18
  outliers final: 13
  residues processed: 122
  average time/residue: 0.1728
  time to fit residues: 29.5321
Evaluate side-chains
  126 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue  149 SER
Chi-restraints excluded: chain R residue  271 THR
Chi-restraints excluded: chain R residue  274 ASP
Chi-restraints excluded: chain R residue  295 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0370
   chunk 28 optimal weight:    4.9990
   chunk 77 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 85 optimal weight:    8.9990
   chunk 14 optimal weight:    6.9990
   chunk 83 optimal weight:    0.9980
   chunk 78 optimal weight:    0.5980
   chunk 88 optimal weight:    4.9990
   overall best weight:    0.6660

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  36 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.186887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.145179 restraints weight = 9069.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.141813 restraints weight = 7943.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.144024 restraints weight = 9410.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
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   0.067   7504  Z= 0.154
  Angle     :  0.529  12.992  10154  Z= 0.275
  Chirality :  0.041   0.168   1139
  Planarity :  0.003   0.038   1282
  Dihedral  :  3.937  30.961   1017
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 16.21 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.28), residues: 910
  helix:  2.22 (0.26), residues: 404
  sheet: -1.25 (0.40), residues: 161
  loop : -1.95 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.009   0.001   HIS A 220 
 PHE   0.036   0.001   PHE R 154 
 TYR   0.019   0.001   TYR A 253 
 ARG   0.004   0.000   ARG B  19 

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 1.969 
Fit side-chains
REVERT: A  317 ARG cc_start: 0.8629 (mpp80) cc_final: 0.7697 (mpp-170)
REVERT: A  343 ASP cc_start: 0.7243 (m-30) cc_final: 0.6964 (m-30)
REVERT: B   75 GLN cc_start: 0.7945 (mm110) cc_final: 0.7560 (mt0)
REVERT: B  175 GLN cc_start: 0.8428 (mt0) cc_final: 0.8107 (mm-40)
REVERT: R   27 TYR cc_start: 0.8648 (m-80) cc_final: 0.8219 (m-80)
REVERT: R  273 MET cc_start: 0.7735 (ptm) cc_final: 0.7530 (ptp)
REVERT: R  302 MET cc_start: 0.6951 (tmm) cc_final: 0.6697 (tmm)
  outliers start: 14
  outliers final: 10
  residues processed: 119
  average time/residue: 0.1895
  time to fit residues: 31.0900
Evaluate side-chains
  112 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 1.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue  149 SER
Chi-restraints excluded: chain R residue  274 ASP
Chi-restraints excluded: chain R residue  295 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 83 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 76 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
B  36 ASN
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.185585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.144301 restraints weight = 9002.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.142670 restraints weight = 7724.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.143994 restraints weight = 8956.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   7504  Z= 0.193
  Angle     :  0.541  12.712  10154  Z= 0.282
  Chirality :  0.041   0.182   1139
  Planarity :  0.003   0.038   1282
  Dihedral  :  3.915  30.032   1017
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 16.21 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.28), residues: 910
  helix:  2.14 (0.25), residues: 404
  sheet: -1.27 (0.40), residues: 165
  loop : -1.85 (0.32), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 339 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.031   0.001   PHE R 165 
 TYR   0.021   0.001   TYR A 253 
 ARG   0.003   0.000   ARG B  19 

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.766 
Fit side-chains
REVERT: A  317 ARG cc_start: 0.8602 (mpp80) cc_final: 0.7722 (mpp-170)
REVERT: A  343 ASP cc_start: 0.7186 (m-30) cc_final: 0.6906 (m-30)
REVERT: R   27 TYR cc_start: 0.8628 (m-80) cc_final: 0.8213 (m-80)
REVERT: R  273 MET cc_start: 0.7724 (ptm) cc_final: 0.7517 (ptp)
REVERT: R  302 MET cc_start: 0.7015 (tmm) cc_final: 0.6733 (tmm)
  outliers start: 18
  outliers final: 10
  residues processed: 122
  average time/residue: 0.2160
  time to fit residues: 37.0254
Evaluate side-chains
  117 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain R residue  149 SER
Chi-restraints excluded: chain R residue  295 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 21 optimal weight:    0.1980
   chunk 41 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 80 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0030
   chunk 10 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 45 optimal weight:   10.0000
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.9794

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

Flipped N/Q/H residues before XYZ refinement:
B  36 ASN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.182170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.123408 restraints weight = 9100.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.128292 restraints weight = 5494.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.131295 restraints weight = 4177.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   7504  Z= 0.185
  Angle     :  0.547  12.547  10154  Z= 0.285
  Chirality :  0.041   0.170   1139
  Planarity :  0.003   0.038   1282
  Dihedral  :  3.925  29.485   1017
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 16.46 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.28), residues: 910
  helix:  2.17 (0.25), residues: 404
  sheet: -1.09 (0.41), residues: 163
  loop : -1.84 (0.31), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 339 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.034   0.001   PHE R 154 
 TYR   0.021   0.001   TYR A 253 
 ARG   0.005   0.000   ARG B  19 

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.857 
Fit side-chains
REVERT: A  317 ARG cc_start: 0.8640 (mpp80) cc_final: 0.7686 (mpp-170)
REVERT: A  343 ASP cc_start: 0.7341 (m-30) cc_final: 0.6904 (m-30)
REVERT: B  175 GLN cc_start: 0.8454 (mt0) cc_final: 0.7968 (mm-40)
REVERT: R   27 TYR cc_start: 0.8821 (m-80) cc_final: 0.8320 (m-80)
REVERT: R  273 MET cc_start: 0.7694 (ptm) cc_final: 0.7491 (ptp)
REVERT: R  302 MET cc_start: 0.7011 (tmm) cc_final: 0.6688 (tmm)
  outliers start: 14
  outliers final: 11
  residues processed: 117
  average time/residue: 0.1727
  time to fit residues: 28.3395
Evaluate side-chains
  113 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue  149 SER
Chi-restraints excluded: chain R residue  295 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 40 optimal weight:   10.0000
   chunk 16 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 58 optimal weight:    5.9990
   chunk 86 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
B  36 ASN
B  88 ASN
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.181502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.139740 restraints weight = 9093.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.137419 restraints weight = 8467.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.139020 restraints weight = 9486.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   7504  Z= 0.286
  Angle     :  0.598  12.346  10154  Z= 0.315
  Chirality :  0.043   0.178   1139
  Planarity :  0.004   0.038   1282
  Dihedral  :  4.095  31.094   1017
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 16.46 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.28), residues: 910
  helix:  2.11 (0.25), residues: 398
  sheet: -1.30 (0.41), residues: 168
  loop : -1.87 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 339 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.030   0.002   PHE R 165 
 TYR   0.020   0.002   TYR A 253 
 ARG   0.004   0.000   ARG B  19 

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.811 
Fit side-chains
REVERT: A  221 MET cc_start: 0.8406 (ttp) cc_final: 0.8125 (ttm)
REVERT: A  343 ASP cc_start: 0.7192 (m-30) cc_final: 0.6940 (m-30)
REVERT: R   27 TYR cc_start: 0.8634 (m-80) cc_final: 0.8213 (m-80)
REVERT: R  273 MET cc_start: 0.7833 (ptm) cc_final: 0.7619 (ptp)
REVERT: R  302 MET cc_start: 0.7049 (tmm) cc_final: 0.6732 (tmm)
  outliers start: 19
  outliers final: 15
  residues processed: 114
  average time/residue: 0.2413
  time to fit residues: 38.7303
Evaluate side-chains
  115 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 1.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain R residue  149 SER
Chi-restraints excluded: chain R residue  269 ILE
Chi-restraints excluded: chain R residue  271 THR
Chi-restraints excluded: chain R residue  274 ASP
Chi-restraints excluded: chain R residue  295 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 80 optimal weight:    0.3980
   chunk 89 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 57 optimal weight:    9.9990
   chunk 66 optimal weight:    0.8980
   chunk 78 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0010
   overall best weight:    0.9988

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

Flipped N/Q/H residues before XYZ refinement:
B  36 ASN
B  88 ASN
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.183858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.141487 restraints weight = 9106.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.140157 restraints weight = 7599.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.141613 restraints weight = 8454.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7504  Z= 0.190
  Angle     :  0.577  13.410  10154  Z= 0.300
  Chirality :  0.042   0.218   1139
  Planarity :  0.003   0.049   1282
  Dihedral  :  4.060  30.059   1017
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 17.71 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.29), residues: 910
  helix:  2.12 (0.26), residues: 404
  sheet: -1.10 (0.42), residues: 164
  loop : -1.81 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 339 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.032   0.001   PHE R 165 
 TYR   0.022   0.001   TYR A 253 
 ARG   0.005   0.000   ARG B  19 

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

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

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1820 Ramachandran restraints generated.
    910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 1.105 
Fit side-chains
REVERT: A  252 SER cc_start: 0.9196 (t) cc_final: 0.8876 (p)
REVERT: A  343 ASP cc_start: 0.7301 (m-30) cc_final: 0.6917 (m-30)
REVERT: R   27 TYR cc_start: 0.8747 (m-80) cc_final: 0.8271 (m-80)
  outliers start: 14
  outliers final: 13
  residues processed: 114
  average time/residue: 0.2497
  time to fit residues: 38.9579
Evaluate side-chains
  115 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain R residue  149 SER
Chi-restraints excluded: chain R residue  271 THR
Chi-restraints excluded: chain R residue  295 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 73 optimal weight:    6.9990
   chunk 81 optimal weight:    7.9990
   chunk 57 optimal weight:    9.9990
   chunk 84 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 76 optimal weight:    0.7980
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
B  36 ASN
B  88 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.183449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.141313 restraints weight = 8964.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.139633 restraints weight = 8232.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.140654 restraints weight = 10404.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7504  Z= 0.210
  Angle     :  0.586  13.338  10154  Z= 0.306
  Chirality :  0.042   0.216   1139
  Planarity :  0.004   0.075   1282
  Dihedral  :  4.043  29.633   1017
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 18.09 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.28), residues: 910
  helix:  2.11 (0.25), residues: 404
  sheet: -1.09 (0.42), residues: 164
  loop : -1.80 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 339 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.032   0.001   PHE R 165 
 TYR   0.021   0.001   TYR A 253 
 ARG   0.010   0.000   ARG B  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2588.01 seconds
wall clock time: 47 minutes 35.79 seconds (2855.79 seconds total)