Starting phenix.real_space_refine
on Sun Mar 17 12:32:56 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp5_27630/03_2024/8dp5_27630_trim_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp5_27630/03_2024/8dp5_27630.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp5_27630/03_2024/8dp5_27630.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp5_27630/03_2024/8dp5_27630.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp5_27630/03_2024/8dp5_27630_trim_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp5_27630/03_2024/8dp5_27630_trim_updated.pdb"
  }
  resolution = 3.1
  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=   0.000 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: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      40      5.16       5
     C    5623      2.51       5
     N    1559      2.21       5
     O    1640      1.98       5
     H    8908      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  195": "OE1" <-> "OE2"
    Residue "A GLU  268": "OE1" <-> "OE2"
    Residue "A GLU  275": "OE1" <-> "OE2"
    Residue "B GLU  259": "OE1" <-> "OE2"
    Residue "C GLU    7": "OE1" <-> "OE2"
    Residue "C GLU   33": "OE1" <-> "OE2"
    Residue "C GLU   37": "OE1" <-> "OE2"
    Residue "C GLU   41": "OE1" <-> "OE2"
    Residue "C GLU   75": "OE1" <-> "OE2"
    Residue "C GLU   83": "OE1" <-> "OE2"
    Residue "C GLU  161": "OE1" <-> "OE2"
    Residue "D GLU   15": "OE1" <-> "OE2"
    Residue "D GLU   36": "OE1" <-> "OE2"
    Residue "D GLU   71": "OE1" <-> "OE2"
    Residue "D GLU   76": "OE1" <-> "OE2"
    Residue "D GLU   84": "OE1" <-> "OE2"
    Residue "D GLU  211": "OE1" <-> "OE2"
    Residue "E ARG   73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 17772
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 5051
          Classifications: {'peptide': 334}
          Link IDs: {'PTRANS': 34, 'TRANS': 299}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5084
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 5084
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 35, 'TRANS': 299}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 3691
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 3691
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 5, 'TRANS': 224}
    Chain: "D"
      Number of atoms: 3698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 3698
          Classifications: {'peptide': 231}
          Link IDs: {'PTRANS': 5, 'TRANS': 225}
    Chain: "E"
      Number of atoms: 136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 136
          Classifications: {'peptide': 8}
          Link IDs: {'PTRANS': 1, 'TRANS': 6}
    Chain: "P"
      Number of atoms: 112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 112
          Classifications: {'peptide': 7}
          Link IDs: {'PTRANS': 1, 'TRANS': 5}
  Time building chain proxies: 8.19, per 1000 atoms: 0.46
  Number of scatterers: 17772
  At special positions: 0
  Unit cell: (79.325, 103.54, 154.475, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      40     16.00
     P       2     15.00
     O    1640      8.00
     N    1559      7.00
     C    5623      6.00
     H    8908      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 14.47
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2142

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      43 helices and 7 sheets defined
      62.1% alpha, 6.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 131 through 157
    Processing helix  chain 'A' and resid 215 through 221
    Processing helix  chain 'A' and resid 262 through 271
      removed outlier: 3.744A  pdb=" N   ALA A 267 " --> pdb=" O   ALA A 263 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLU A 268 " --> pdb=" O   GLN A 264 " (cutoff:3.500A)
      removed outlier: 5.550A  pdb=" N   THR A 271 " --> pdb=" O   ALA A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 298
      removed outlier: 3.984A  pdb=" N   TRP A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ALA A 290 " --> pdb=" O   LEU A 286 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   PHE A 294 " --> pdb=" O   ALA A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 309
      No H-bonds generated for 'chain 'A' and resid 307 through 309'
    Processing helix  chain 'A' and resid 331 through 333
      No H-bonds generated for 'chain 'A' and resid 331 through 333'
    Processing helix  chain 'A' and resid 349 through 362
      removed outlier: 3.782A  pdb=" N   ARG A 357 " --> pdb=" O   GLY A 353 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   LEU A 362 " --> pdb=" O   ALA A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 384
      removed outlier: 3.516A  pdb=" N   ALA A 379 " --> pdb=" O   GLU A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 399
    Processing helix  chain 'A' and resid 420 through 441
    Processing helix  chain 'A' and resid 447 through 456
    Processing helix  chain 'A' and resid 461 through 472
    Processing helix  chain 'B' and resid 131 through 157
    Processing helix  chain 'B' and resid 215 through 223
      removed outlier: 3.756A  pdb=" N   ALA B 222 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 269
    Processing helix  chain 'B' and resid 277 through 297
    Processing helix  chain 'B' and resid 331 through 333
      No H-bonds generated for 'chain 'B' and resid 331 through 333'
    Processing helix  chain 'B' and resid 349 through 362
    Processing helix  chain 'B' and resid 369 through 384
      removed outlier: 3.547A  pdb=" N   THR B 382 " --> pdb=" O   ALA B 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 399
      removed outlier: 3.506A  pdb=" N   GLY B 393 " --> pdb=" O   SER B 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 420 through 440
    Processing helix  chain 'B' and resid 447 through 457
    Processing helix  chain 'B' and resid 461 through 471
    Processing helix  chain 'C' and resid 5 through 17
    Processing helix  chain 'C' and resid 21 through 34
      removed outlier: 4.089A  pdb=" N   GLN C  34 " --> pdb=" O   ALA C  30 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 70
      removed outlier: 3.611A  pdb=" N   ALA C  56 " --> pdb=" O   ASN C  52 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   ARG C  57 " --> pdb=" O   VAL C  53 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 75 through 105
      removed outlier: 4.335A  pdb=" N   MET C  80 " --> pdb=" O   LYS C  76 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   GLU C  83 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLU C  91 " --> pdb=" O   LYS C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 107 through 110
      No H-bonds generated for 'chain 'C' and resid 107 through 110'
    Processing helix  chain 'C' and resid 114 through 134
      removed outlier: 4.066A  pdb=" N   VAL C 134 " --> pdb=" O   TYR C 130 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 161
      removed outlier: 3.527A  pdb=" N   THR C 142 " --> pdb=" O   ASN C 139 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLN C 149 " --> pdb=" O   ASN C 146 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLN C 152 " --> pdb=" O   GLN C 149 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLU C 156 " --> pdb=" O   GLU C 153 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   LYS C 159 " --> pdb=" O   GLU C 156 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   GLU C 161 " --> pdb=" O   SER C 158 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 182
    Processing helix  chain 'C' and resid 187 through 207
      removed outlier: 4.183A  pdb=" N   GLU C 204 " --> pdb=" O   GLU C 200 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LEU C 205 " --> pdb=" O   ALA C 201 " (cutoff:3.500A)
      removed outlier: 5.454A  pdb=" N   ASP C 206 " --> pdb=" O   ILE C 202 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   THR C 207 " --> pdb=" O   ALA C 203 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 210 through 231
      removed outlier: 4.495A  pdb=" N   ASP C 215 " --> pdb=" O   GLU C 211 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   LEU C 222 " --> pdb=" O   LEU C 218 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 4 through 16
    Processing helix  chain 'D' and resid 20 through 33
      removed outlier: 3.655A  pdb=" N   GLU D  25 " --> pdb=" O   ASP D  21 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL D  30 " --> pdb=" O   SER D  26 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   MET D  33 " --> pdb=" O   LYS D  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 39 through 70
      removed outlier: 4.043A  pdb=" N   ARG D  56 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 76 through 106
    Processing helix  chain 'D' and resid 108 through 111
      No H-bonds generated for 'chain 'D' and resid 108 through 111'
    Processing helix  chain 'D' and resid 115 through 135
      removed outlier: 3.696A  pdb=" N   LEU D 132 " --> pdb=" O   TYR D 128 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   PHE D 135 " --> pdb=" O   TYR D 131 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 138 through 162
      removed outlier: 3.829A  pdb=" N   GLU D 143 " --> pdb=" O   ASP D 140 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA D 144 " --> pdb=" O   ARG D 141 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLU D 146 " --> pdb=" O   GLU D 143 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   SER D 148 " --> pdb=" O   ALA D 145 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   VAL D 150 " --> pdb=" O   ASN D 147 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ASP D 157 " --> pdb=" O   ALA D 154 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ILE D 158 " --> pdb=" O   ALA D 155 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   MET D 160 " --> pdb=" O   ASP D 157 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 168 through 183
    Processing helix  chain 'D' and resid 188 through 208
      removed outlier: 3.719A  pdb=" N   ALA D 204 " --> pdb=" O   ASP D 200 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   GLU D 205 " --> pdb=" O   ASP D 201 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU D 206 " --> pdb=" O   ALA D 202 " (cutoff:3.500A)
      removed outlier: 5.499A  pdb=" N   ASP D 207 " --> pdb=" O   ILE D 203 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   THR D 208 " --> pdb=" O   ALA D 204 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 211 through 232
      removed outlier: 4.002A  pdb=" N   ASP D 216 " --> pdb=" O   GLU D 212 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU D 219 " --> pdb=" O   LYS D 215 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ILE D 220 " --> pdb=" O   ASP D 216 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 170 through 173
      removed outlier: 4.401A  pdb=" N   ALA A 252 " --> pdb=" O   LYS A 204 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   GLY A 235 " --> pdb=" O   LEU A 253 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 300 through 302
    Processing sheet with id=  C, first strand: chain 'A' and resid 310 through 313
    Processing sheet with id=  D, first strand: chain 'B' and resid 170 through 173
    Processing sheet with id=  E, first strand: chain 'B' and resid 300 through 302
    Processing sheet with id=  F, first strand: chain 'B' and resid 311 through 313
    Processing sheet with id=  G, first strand: chain 'B' and resid 233 through 237
      removed outlier: 6.908A  pdb=" N   LEU B 253 " --> pdb=" O   CYS B 234 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   LEU B 236 " --> pdb=" O   VAL B 251 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   VAL B 251 " --> pdb=" O   LEU B 236 " (cutoff:3.500A)

    538 hydrogen bonds defined for protein.
    1500 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: 6.15

  Time building geometry restraints manager: 14.99 seconds

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

  Histogram of bond lengths:
        0.87 -     1.07: 1917
        1.07 -     1.26: 8450
        1.26 -     1.45: 2272
        1.45 -     1.64: 5273
        1.64 -     1.83: 59
  Bond restraints: 17971
  Sorted by residual:
  bond pdb=" N   ILE D  66 "
       pdb=" H   ILE D  66 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.74e+01
  bond pdb=" CE3 TRP A 279 "
       pdb=" HE3 TRP A 279 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.72e+01
  bond pdb=" N   THR D 137 "
       pdb=" H   THR D 137 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" N   GLN A 466 "
       pdb=" H   GLN A 466 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" N   ALA C 201 "
       pdb=" H   ALA C 201 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  ... (remaining 17966 not shown)

  Histogram of bond angle deviations from ideal:
       95.68 -   103.57: 182
      103.57 -   111.45: 19249
      111.45 -   119.33: 6917
      119.33 -   127.22: 6128
      127.22 -   135.10: 144
  Bond angle restraints: 32620
  Sorted by residual:
  angle pdb=" N   PRO B 338 "
        pdb=" CA  PRO B 338 "
        pdb=" C   PRO B 338 "
      ideal   model   delta    sigma   weight residual
     110.70  119.15   -8.45 1.22e+00 6.72e-01 4.79e+01
  angle pdb=" N   ALA A 291 "
        pdb=" CA  ALA A 291 "
        pdb=" C   ALA A 291 "
      ideal   model   delta    sigma   weight residual
     111.69  103.67    8.02 1.23e+00 6.61e-01 4.26e+01
  angle pdb=" C   LEU D 163 "
        pdb=" N   PRO D 164 "
        pdb=" CA  PRO D 164 "
      ideal   model   delta    sigma   weight residual
     119.66  124.04   -4.38 7.30e-01 1.88e+00 3.60e+01
  angle pdb=" CA  GLU B 132 "
        pdb=" C   GLU B 132 "
        pdb=" O   GLU B 132 "
      ideal   model   delta    sigma   weight residual
     120.90  114.84    6.06 1.03e+00 9.43e-01 3.47e+01
  angle pdb=" CA  PRO B 338 "
        pdb=" C   PRO B 338 "
        pdb=" N   PRO B 339 "
      ideal   model   delta    sigma   weight residual
     117.93  124.70   -6.77 1.20e+00 6.94e-01 3.18e+01
  ... (remaining 32615 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 7795
       17.94 -    35.88: 362
       35.88 -    53.82: 189
       53.82 -    71.75: 93
       71.75 -    89.69: 9
  Dihedral angle restraints: 8448
    sinusoidal: 4687
      harmonic: 3761
  Sorted by residual:
  dihedral pdb=" CA  GLY B 343 "
           pdb=" C   GLY B 343 "
           pdb=" N   SER B 344 "
           pdb=" CA  SER B 344 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.21   27.79     0      5.00e+00 4.00e-02 3.09e+01
  dihedral pdb=" CA  ASP B 196 "
           pdb=" C   ASP B 196 "
           pdb=" N   ALA B 197 "
           pdb=" CA  ALA B 197 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.85   25.15     0      5.00e+00 4.00e-02 2.53e+01
  dihedral pdb=" CA  ASP A 196 "
           pdb=" C   ASP A 196 "
           pdb=" N   ALA A 197 "
           pdb=" CA  ALA A 197 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.45   24.55     0      5.00e+00 4.00e-02 2.41e+01
  ... (remaining 8445 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 970
       0.089 -    0.178: 345
       0.178 -    0.267: 60
       0.267 -    0.357: 7
       0.357 -    0.446: 2
  Chirality restraints: 1384
  Sorted by residual:
  chirality pdb=" CA  LYS D  73 "
            pdb=" N   LYS D  73 "
            pdb=" C   LYS D  73 "
            pdb=" CB  LYS D  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 4.97e+00
  chirality pdb=" CA  LEU B 253 "
            pdb=" N   LEU B 253 "
            pdb=" C   LEU B 253 "
            pdb=" CB  LEU B 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.21e+00
  chirality pdb=" CA  ASN D 186 "
            pdb=" N   ASN D 186 "
            pdb=" C   ASN D 186 "
            pdb=" CB  ASN D 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.77e+00
  ... (remaining 1381 not shown)

  Planarity restraints: 2653
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 472 "    0.216 2.00e-02 2.50e+03   7.21e-02 2.08e+02
        pdb=" CG  TRP A 472 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 472 "   -0.050 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 472 "   -0.051 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 472 "   -0.059 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 472 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 472 "   -0.067 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 472 "    0.028 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 472 "   -0.018 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 472 "    0.037 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 472 "    0.007 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 472 "   -0.043 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 472 "   -0.093 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 472 "    0.057 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 472 "   -0.009 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 472 "    0.079 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 423 "    0.165 2.00e-02 2.50e+03   6.57e-02 1.73e+02
        pdb=" CG  TRP B 423 "    0.003 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 423 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 423 "   -0.047 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 423 "   -0.063 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 423 "   -0.037 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 423 "   -0.066 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 423 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 423 "   -0.015 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 423 "    0.041 2.00e-02 2.50e+03
        pdb=" HD1 TRP B 423 "    0.045 2.00e-02 2.50e+03
        pdb=" HE1 TRP B 423 "   -0.067 2.00e-02 2.50e+03
        pdb=" HE3 TRP B 423 "   -0.093 2.00e-02 2.50e+03
        pdb=" HZ2 TRP B 423 "    0.037 2.00e-02 2.50e+03
        pdb=" HZ3 TRP B 423 "   -0.008 2.00e-02 2.50e+03
        pdb=" HH2 TRP B 423 "    0.106 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D  60 "   -0.152 2.00e-02 2.50e+03   6.14e-02 1.51e+02
        pdb=" CG  TRP D  60 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD1 TRP D  60 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP D  60 "    0.021 2.00e-02 2.50e+03
        pdb=" NE1 TRP D  60 "    0.047 2.00e-02 2.50e+03
        pdb=" CE2 TRP D  60 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP D  60 "    0.049 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D  60 "   -0.036 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D  60 "    0.018 2.00e-02 2.50e+03
        pdb=" CH2 TRP D  60 "   -0.040 2.00e-02 2.50e+03
        pdb=" HD1 TRP D  60 "   -0.021 2.00e-02 2.50e+03
        pdb=" HE1 TRP D  60 "    0.106 2.00e-02 2.50e+03
        pdb=" HE3 TRP D  60 "    0.089 2.00e-02 2.50e+03
        pdb=" HZ2 TRP D  60 "   -0.056 2.00e-02 2.50e+03
        pdb=" HZ3 TRP D  60 "    0.033 2.00e-02 2.50e+03
        pdb=" HH2 TRP D  60 "   -0.069 2.00e-02 2.50e+03
  ... (remaining 2650 not shown)

  Histogram of nonbonded interaction distances:
        1.29 -     1.95: 288
        1.95 -     2.61: 17168
        2.61 -     3.28: 53847
        3.28 -     3.94: 67894
        3.94 -     4.60: 100115
  Nonbonded interactions: 239312
  Sorted by model distance:
  nonbonded pdb="HD11 LEU C 205 "
            pdb=" HD1 TYR C 213 "
     model   vdw
     1.288 2.270
  nonbonded pdb=" OE2 GLU D 183 "
            pdb=" HG1 THR P  67 "
     model   vdw
     1.548 1.850
  nonbonded pdb="HD21 LEU A 356 "
            pdb=" HB1 ALA A 378 "
     model   vdw
     1.582 2.440
  nonbonded pdb=" HG  SER D 210 "
            pdb=" OE2 GLU D 212 "
     model   vdw
     1.595 1.850
  nonbonded pdb=" OE2 GLU D  36 "
            pdb=" HG  SER D 117 "
     model   vdw
     1.601 1.850
  ... (remaining 239307 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 130 through 472)
  selection = (chain 'B' and (resid 130 through 406 or resid 419 through 472))
}
ncs_group {
  reference = (chain 'E' and resid 66 through 72)
  selection = chain 'P'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.990
  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:             0.270
  Extract box with map and model:          7.840
  Check model and map are aligned:         0.280
  Set scattering table:                    0.170
  Process input model:                     58.860
  Find NCS groups from input model:        0.570
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   73.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
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      :  0.013   0.140   9063  Z= 0.856
  Angle     :  1.783  12.815  12331  Z= 1.232
  Chirality :  0.089   0.446   1384
  Planarity :  0.016   0.192   1598
  Dihedral  : 12.279  89.692   3379
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 0.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.19 %
  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: -0.51 (0.22), residues: 1123
  helix: -0.23 (0.16), residues: 707
  sheet:  0.71 (0.60), residues: 82
  loop : -0.48 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.149   0.019   TRP A 472 
 HIS   0.010   0.002   HIS A 166 
 PHE   0.041   0.009   PHE C 176 
 TYR   0.134   0.015   TYR C 127 
 ARG   0.013   0.001   ARG A 333 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 925 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 1.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  175 ASP cc_start: 0.6794 (t0) cc_final: 0.6534 (t0)
REVERT: B  207 LYS cc_start: 0.7442 (tttt) cc_final: 0.7215 (tttp)
REVERT: C  193 LEU cc_start: 0.7334 (tp) cc_final: 0.7036 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.6283
  time to fit residues: 107.9010
Evaluate side-chains
  65 residues out of total 925 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 1.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 28 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 87 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   chunk 101 optimal weight:    0.7980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 135 HIS
B 135 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9063  Z= 0.255
  Angle     :  0.640   7.567  12331  Z= 0.340
  Chirality :  0.036   0.137   1384
  Planarity :  0.006   0.060   1598
  Dihedral  :  5.330  32.611   1250
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  3.24 %
    Favored  : 96.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.25), residues: 1123
  helix:  1.59 (0.19), residues: 707
  sheet: -0.47 (0.54), residues: 97
  loop : -0.22 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 472 
 HIS   0.011   0.002   HIS C 166 
 PHE   0.015   0.002   PHE D 177 
 TYR   0.017   0.002   TYR C 127 
 ARG   0.005   0.001   ARG B 427 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 925 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 1.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  175 ASP cc_start: 0.6811 (t0) cc_final: 0.6474 (t0)
REVERT: B  207 LYS cc_start: 0.7392 (tttt) cc_final: 0.7179 (tttp)
  outliers start: 4
  outliers final: 2
  residues processed: 76
  average time/residue: 0.6211
  time to fit residues: 61.8531
Evaluate side-chains
  60 residues out of total 925 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 58
  time to evaluate  : 1.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  262 VAL
Chi-restraints excluded: chain C residue   76 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0970
   chunk 69 optimal weight:    3.9990
   chunk 28 optimal weight:    0.3980
   chunk 101 optimal weight:    1.9990
   chunk 110 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9063  Z= 0.187
  Angle     :  0.535   6.452  12331  Z= 0.274
  Chirality :  0.035   0.142   1384
  Planarity :  0.005   0.052   1598
  Dihedral  :  4.753  37.744   1250
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 1.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  3.68 %
    Favored  : 96.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.25), residues: 1123
  helix:  2.16 (0.19), residues: 711
  sheet: -0.84 (0.52), residues: 99
  loop : -0.34 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 472 
 HIS   0.008   0.001   HIS B 166 
 PHE   0.012   0.001   PHE D 120 
 TYR   0.015   0.001   TYR C 127 
 ARG   0.005   0.000   ARG B 438 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 925 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 1.326 
Fit side-chains
   revert: symmetry clash
REVERT: B  175 ASP cc_start: 0.6739 (t0) cc_final: 0.6488 (t70)
REVERT: B  207 LYS cc_start: 0.7353 (tttt) cc_final: 0.7145 (tttp)
REVERT: C  215 ASP cc_start: 0.7733 (m-30) cc_final: 0.7166 (t70)
  outliers start: 3
  outliers final: 1
  residues processed: 65
  average time/residue: 0.6366
  time to fit residues: 53.6276
Evaluate side-chains
  55 residues out of total 925 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 1.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  166 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9980
   chunk 108 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 96 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    1.3384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.3234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9063  Z= 0.242
  Angle     :  0.523   7.547  12331  Z= 0.267
  Chirality :  0.035   0.136   1384
  Planarity :  0.005   0.048   1598
  Dihedral  :  4.548  36.534   1250
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  4.65 %
    Favored  : 95.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.95 (0.25), residues: 1123
  helix:  2.33 (0.19), residues: 714
  sheet: -0.92 (0.50), residues: 99
  loop : -0.38 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 472 
 HIS   0.008   0.001   HIS B 166 
 PHE   0.012   0.001   PHE D 120 
 TYR   0.015   0.001   TYR C 127 
 ARG   0.005   0.000   ARG B 438 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 925 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 1.494 
Fit side-chains
REVERT: A  196 ASP cc_start: 0.7435 (t0) cc_final: 0.7198 (t0)
REVERT: B  171 PHE cc_start: 0.8143 (m-80) cc_final: 0.7899 (m-80)
REVERT: C  215 ASP cc_start: 0.7853 (m-30) cc_final: 0.7319 (t70)
  outliers start: 3
  outliers final: 2
  residues processed: 59
  average time/residue: 0.6661
  time to fit residues: 51.1075
Evaluate side-chains
  58 residues out of total 925 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 1.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain C residue  218 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 44 optimal weight:    6.9990
   chunk 92 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 27 optimal weight:    0.4980
   chunk 36 optimal weight:    9.9990
   overall best weight:    1.2784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.3406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9063  Z= 0.224
  Angle     :  0.501   6.792  12331  Z= 0.255
  Chirality :  0.034   0.137   1384
  Planarity :  0.005   0.043   1598
  Dihedral  :  4.468  37.140   1250
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  5.08 %
    Favored  : 94.49 %
  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:  2.08 (0.25), residues: 1123
  helix:  2.45 (0.19), residues: 714
  sheet: -0.96 (0.50), residues: 99
  loop : -0.36 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 472 
 HIS   0.008   0.001   HIS B 166 
 PHE   0.012   0.001   PHE D 120 
 TYR   0.014   0.001   TYR C 127 
 ARG   0.006   0.000   ARG B 438 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 925 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 1.310 
Fit side-chains
   revert: symmetry clash
REVERT: A  196 ASP cc_start: 0.7468 (t0) cc_final: 0.7193 (t0)
REVERT: B  171 PHE cc_start: 0.8138 (m-80) cc_final: 0.7927 (m-80)
REVERT: C  215 ASP cc_start: 0.7829 (m-30) cc_final: 0.7239 (t70)
  outliers start: 4
  outliers final: 3
  residues processed: 60
  average time/residue: 0.6541
  time to fit residues: 51.6655
Evaluate side-chains
  59 residues out of total 925 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 1.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain C residue  193 LEU
Chi-restraints excluded: chain C residue  218 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 21 optimal weight:    0.2980
   chunk 63 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 108 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9980
   chunk 50 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 104 optimal weight:    0.6980
   overall best weight:    0.7582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.3578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9063  Z= 0.156
  Angle     :  0.469   6.112  12331  Z= 0.236
  Chirality :  0.034   0.136   1384
  Planarity :  0.004   0.046   1598
  Dihedral  :  4.285  43.097   1250
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  6.38 %
    Favored  : 93.51 %
  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:  2.42 (0.26), residues: 1123
  helix:  2.70 (0.19), residues: 715
  sheet: -0.91 (0.50), residues: 99
  loop : -0.17 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 230 
 HIS   0.008   0.001   HIS B 166 
 PHE   0.009   0.001   PHE D 120 
 TYR   0.012   0.001   TYR C 127 
 ARG   0.007   0.000   ARG B 438 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 925 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 66
  time to evaluate  : 1.420 
Fit side-chains
   revert: symmetry clash
REVERT: A  196 ASP cc_start: 0.7459 (t0) cc_final: 0.7193 (t0)
REVERT: B  175 ASP cc_start: 0.5857 (m-30) cc_final: 0.5254 (p0)
REVERT: C  215 ASP cc_start: 0.7799 (m-30) cc_final: 0.7366 (t70)
  outliers start: 1
  outliers final: 1
  residues processed: 66
  average time/residue: 0.6545
  time to fit residues: 55.7459
Evaluate side-chains
  60 residues out of total 925 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 1.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  166 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 107 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   overall best weight:    1.0986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.3711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9063  Z= 0.209
  Angle     :  0.481   5.773  12331  Z= 0.242
  Chirality :  0.035   0.201   1384
  Planarity :  0.004   0.042   1598
  Dihedral  :  4.257  43.458   1250
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  6.49 %
    Favored  : 93.19 %
  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:  2.38 (0.25), residues: 1123
  helix:  2.70 (0.19), residues: 715
  sheet: -1.00 (0.49), residues: 99
  loop : -0.23 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 230 
 HIS   0.008   0.001   HIS B 166 
 PHE   0.010   0.001   PHE D 120 
 TYR   0.014   0.001   TYR C 127 
 ARG   0.006   0.000   ARG B 438 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 925 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 1.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 ASP cc_start: 0.7471 (t0) cc_final: 0.7225 (t0)
REVERT: B  175 ASP cc_start: 0.5701 (m-30) cc_final: 0.5321 (p0)
REVERT: C  215 ASP cc_start: 0.7842 (m-30) cc_final: 0.7336 (t70)
  outliers start: 3
  outliers final: 2
  residues processed: 63
  average time/residue: 0.6411
  time to fit residues: 52.9062
Evaluate side-chains
  64 residues out of total 925 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 1.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain C residue  193 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0670
   chunk 20 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 84 optimal weight:    0.5980
   chunk 98 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9990
   overall best weight:    0.6318

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.3823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9063  Z= 0.144
  Angle     :  0.455   5.749  12331  Z= 0.227
  Chirality :  0.033   0.137   1384
  Planarity :  0.004   0.048   1598
  Dihedral  :  4.154  50.532   1250
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 2.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  6.59 %
    Favored  : 93.19 %
  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:  2.65 (0.26), residues: 1123
  helix:  2.90 (0.19), residues: 715
  sheet: -1.00 (0.49), residues: 99
  loop : -0.06 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 230 
 HIS   0.008   0.001   HIS B 166 
 PHE   0.008   0.001   PHE B 171 
 TYR   0.011   0.001   TYR C 127 
 ARG   0.008   0.000   ARG B 438 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 925 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 1.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 ASP cc_start: 0.7454 (t0) cc_final: 0.7195 (t0)
REVERT: B  175 ASP cc_start: 0.5785 (m-30) cc_final: 0.5428 (p0)
REVERT: C  215 ASP cc_start: 0.7824 (m-30) cc_final: 0.7312 (t70)
  outliers start: 2
  outliers final: 2
  residues processed: 66
  average time/residue: 0.6288
  time to fit residues: 55.1856
Evaluate side-chains
  65 residues out of total 925 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 1.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain C residue  193 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   chunk 78 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 90 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 106 optimal weight:    1.9990
   overall best weight:    1.0784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.3886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9063  Z= 0.206
  Angle     :  0.469   5.771  12331  Z= 0.234
  Chirality :  0.034   0.136   1384
  Planarity :  0.004   0.046   1598
  Dihedral  :  4.161  50.479   1250
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  6.81 %
    Favored  : 92.86 %
  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:  2.57 (0.26), residues: 1123
  helix:  2.85 (0.19), residues: 714
  sheet: -1.08 (0.48), residues: 99
  loop : -0.09 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 472 
 HIS   0.008   0.001   HIS B 166 
 PHE   0.010   0.001   PHE D 120 
 TYR   0.014   0.001   TYR C 127 
 ARG   0.008   0.000   ARG B 438 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 925 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 1.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 ASP cc_start: 0.7476 (t0) cc_final: 0.7237 (t0)
REVERT: B  175 ASP cc_start: 0.5725 (m-30) cc_final: 0.5522 (p0)
REVERT: C  215 ASP cc_start: 0.7856 (m-30) cc_final: 0.7326 (t70)
  outliers start: 3
  outliers final: 2
  residues processed: 67
  average time/residue: 0.6131
  time to fit residues: 53.8456
Evaluate side-chains
  65 residues out of total 925 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 1.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain C residue  193 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0670
   chunk 73 optimal weight:    0.0070
   chunk 111 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9980
   overall best weight:    0.5338

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.3959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9063  Z= 0.135
  Angle     :  0.447   5.739  12331  Z= 0.222
  Chirality :  0.033   0.135   1384
  Planarity :  0.004   0.058   1598
  Dihedral  :  4.116  57.267   1250
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  7.14 %
    Favored  : 92.65 %
  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:  2.77 (0.26), residues: 1123
  helix:  2.99 (0.19), residues: 716
  sheet: -1.06 (0.48), residues: 99
  loop :  0.03 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 472 
 HIS   0.008   0.001   HIS B 166 
 PHE   0.007   0.001   PHE D 120 
 TYR   0.011   0.001   TYR C 127 
 ARG   0.007   0.000   ARG B 438 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 925 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 1.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  196 ASP cc_start: 0.7479 (t0) cc_final: 0.7253 (t0)
REVERT: B  175 ASP cc_start: 0.5880 (m-30) cc_final: 0.5651 (p0)
REVERT: C  215 ASP cc_start: 0.7841 (m-30) cc_final: 0.7321 (t70)
  outliers start: 2
  outliers final: 2
  residues processed: 64
  average time/residue: 0.6475
  time to fit residues: 54.2408
Evaluate side-chains
  63 residues out of total 925 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 1.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  166 HIS
Chi-restraints excluded: chain C residue  193 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 81 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 37 optimal weight:   10.0000
   chunk 91 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0570
   overall best weight:    0.6898

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.138938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.100271 restraints weight = 36985.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 2.82
r_work: 0.3271 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.4010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9063  Z= 0.158
  Angle     :  0.451   5.681  12331  Z= 0.224
  Chirality :  0.033   0.136   1384
  Planarity :  0.004   0.055   1598
  Dihedral  :  4.106  59.617   1250
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  7.24 %
    Favored  : 92.54 %
  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:  2.78 (0.26), residues: 1123
  helix:  3.01 (0.19), residues: 715
  sheet: -1.07 (0.48), residues: 99
  loop :  0.02 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 230 
 HIS   0.008   0.001   HIS B 166 
 PHE   0.008   0.001   PHE D 120 
 TYR   0.015   0.001   TYR C 181 
 ARG   0.009   0.000   ARG B 438 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3652.17 seconds
wall clock time: 65 minutes 2.16 seconds (3902.16 seconds total)