Starting phenix.real_space_refine
on Tue Dec 12 22:59:21 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adi_15363/12_2023/8adi_15363_trim_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adi_15363/12_2023/8adi_15363.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adi_15363/12_2023/8adi_15363.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adi_15363/12_2023/8adi_15363.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adi_15363/12_2023/8adi_15363_trim_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adi_15363/12_2023/8adi_15363_trim_updated.pdb"
  }
  resolution = 3.4
  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=   0.006 sd=   0.094
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    7425      2.51       5
     N    2014      2.21       5
     O    2317      1.98       5
     H   11353      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR  142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  383": "OD1" <-> "OD2"
    Residue "A PHE  675": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  727": "OD1" <-> "OD2"
    Residue "B ASP  288": "OD1" <-> "OD2"
    Residue "C GLU   49": "OE1" <-> "OE2"
    Residue "C ASP   81": "OD1" <-> "OD2"
    Residue "D TYR  205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 23141
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 12144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 786, 12144
          Classifications: {'peptide': 786}
          Link IDs: {'PTRANS': 29, 'TRANS': 756}
    Chain: "B"
      Number of atoms: 5393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 361, 5393
          Classifications: {'peptide': 361}
          Link IDs: {'PTRANS': 11, 'TRANS': 349}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 845
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 6, 'TRANS': 51}
    Chain: "D"
      Number of atoms: 3348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 3348
          Classifications: {'peptide': 209}
          Link IDs: {'PTRANS': 12, 'TRANS': 196}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1292
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 5, 'TRANS': 78}
    Chain: "F"
      Number of atoms: 119
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 119
          Classifications: {'peptide': 7}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'0AF:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 10.38, per 1000 atoms: 0.45
  Number of scatterers: 23141
  At special positions: 0
  Unit cell: (100.3, 133.45, 124.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     O    2317      8.00
     N    2014      7.00
     C    7425      6.00
     H   11353      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 690 " - pdb=" SG  CYS A 700 " distance=2.03

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 17.37
  Conformation dependent library (CDL) restraints added in 2.4 seconds
  

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2754

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      27 helices and 17 sheets defined
      19.5% alpha, 25.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 45
    Processing helix  chain 'A' and resid 56 through 68
    Processing helix  chain 'A' and resid 107 through 117
    Processing helix  chain 'A' and resid 130 through 144
    Processing helix  chain 'A' and resid 190 through 196
      removed outlier: 4.118A  pdb=" N   HIS A 196 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 231
    Processing helix  chain 'A' and resid 281 through 284
      No H-bonds generated for 'chain 'A' and resid 281 through 284'
    Processing helix  chain 'A' and resid 299 through 315
      removed outlier: 3.817A  pdb=" N   TYR A 315 " --> pdb=" O   LEU A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 368
      removed outlier: 4.412A  pdb=" N   GLU A 368 " --> pdb=" O   VAL A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 392
    Processing helix  chain 'A' and resid 449 through 451
      No H-bonds generated for 'chain 'A' and resid 449 through 451'
    Processing helix  chain 'A' and resid 497 through 499
      No H-bonds generated for 'chain 'A' and resid 497 through 499'
    Processing helix  chain 'A' and resid 543 through 546
      No H-bonds generated for 'chain 'A' and resid 543 through 546'
    Processing helix  chain 'A' and resid 648 through 650
      No H-bonds generated for 'chain 'A' and resid 648 through 650'
    Processing helix  chain 'A' and resid 692 through 694
      No H-bonds generated for 'chain 'A' and resid 692 through 694'
    Processing helix  chain 'C' and resid 33 through 36
      No H-bonds generated for 'chain 'C' and resid 33 through 36'
    Processing helix  chain 'D' and resid 32 through 45
    Processing helix  chain 'D' and resid 49 through 61
      removed outlier: 3.650A  pdb=" N   THR D  53 " --> pdb=" O   ARG D  49 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 68 through 81
    Processing helix  chain 'D' and resid 85 through 98
    Processing helix  chain 'D' and resid 106 through 120
    Processing helix  chain 'D' and resid 138 through 153
    Processing helix  chain 'D' and resid 160 through 188
      removed outlier: 3.636A  pdb=" N   PHE D 169 " --> pdb=" O   LYS D 165 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 193 through 204
    Processing helix  chain 'D' and resid 209 through 224
      Proline residue:  D 216  - end of helix
    Processing helix  chain 'D' and resid 228 through 239
    Processing helix  chain 'E' and resid 52 through 58
    Processing sheet with id=  A, first strand: chain 'A' and resid 97 through 100
      removed outlier: 8.936A  pdb=" N   THR A  98 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   LEU A 165 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
      removed outlier: 8.534A  pdb=" N   SER A 100 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LEU A 167 " --> pdb=" O   SER A 100 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'A' and resid 273 through 276
      removed outlier: 6.336A  pdb=" N   VAL A 339 " --> pdb=" O   SER A 274 " (cutoff:3.500A)
      removed outlier: 8.297A  pdb=" N   ASN A 276 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   VAL A 341 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 327 through 329
    Processing sheet with id=  D, first strand: chain 'A' and resid 425 through 431
      removed outlier: 3.545A  pdb=" N   THR A 474 " --> pdb=" O   ALA A 455 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLN A 466 " --> pdb=" O   ASN A 463 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLY A 516 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   TYR A 531 " --> pdb=" O   THR A 511 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ALA A 527 " --> pdb=" O   LEU A 515 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ARG A 526 " --> pdb=" O   GLY A 575 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   VAL A 599 " --> pdb=" O   PHE A 572 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   TYR A 574 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   GLY A 590 " --> pdb=" O   TYR A 618 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ALA A 770 " --> pdb=" O   GLN A 789 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'A' and resid 490 through 495
    Processing sheet with id=  F, first strand: chain 'A' and resid 72 through 79
      removed outlier: 6.856A  pdb=" N   LYS A  89 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   VAL A  75 " --> pdb=" O   GLN A  87 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   GLN A  87 " --> pdb=" O   VAL A  75 " (cutoff:3.500A)
      removed outlier: 5.164A  pdb=" N   VAL A  77 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   LEU A  85 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'A' and resid 176 through 183
      removed outlier: 7.363A  pdb=" N   VAL A 256 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   ILE A 180 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   VAL A 258 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 4.837A  pdb=" N   ILE A 182 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 7.173A  pdb=" N   ILE A 260 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   THR A 261 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 5.399A  pdb=" N   ILE A 240 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'A' and resid 348 through 355
      removed outlier: 7.338A  pdb=" N   VAL A 414 " --> pdb=" O   ARG A 350 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   ILE A 352 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   TYR A 416 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   PHE A 354 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 7.382A  pdb=" N   VAL A 418 " --> pdb=" O   PHE A 354 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   THR A 397 " --> pdb=" O   LYS A 419 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'B' and resid 49 through 51
      removed outlier: 4.041A  pdb=" N   LEU B 378 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'B' and resid 72 through 75
      removed outlier: 3.890A  pdb=" N   TRP B  93 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'B' and resid 122 through 124
      removed outlier: 3.583A  pdb=" N   TRP B 143 " --> pdb=" O   ALA B 133 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'B' and resid 156 through 158
      removed outlier: 3.689A  pdb=" N   TRP B 183 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   ASN B 175 " --> pdb=" O   VAL B 181 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   VAL B 181 " --> pdb=" O   ASN B 175 " (cutoff:3.500A)
    Processing sheet with id=  M, first strand: chain 'B' and resid 206 through 210
      removed outlier: 3.676A  pdb=" N   TRP B 228 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   LEU B 220 " --> pdb=" O   MET B 226 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   MET B 226 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'B' and resid 252 through 254
      removed outlier: 3.697A  pdb=" N   TRP B 279 " --> pdb=" O   ALA B 269 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ASP B 271 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   ILE B 277 " --> pdb=" O   ASP B 271 " (cutoff:3.500A)
    Processing sheet with id=  O, first strand: chain 'B' and resid 290 through 292
      removed outlier: 4.011A  pdb=" N   TRP B 317 " --> pdb=" O   ALA B 307 " (cutoff:3.500A)
    Processing sheet with id=  P, first strand: chain 'B' and resid 331 through 333
    Processing sheet with id=  Q, first strand: chain 'E' and resid 32 through 34

    451 hydrogen bonds defined for protein.
    1257 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: 8.95

  Time building geometry restraints manager: 18.01 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 11328
        1.03 -     1.22: 26
        1.22 -     1.42: 5211
        1.42 -     1.61: 6772
        1.61 -     1.81: 62
  Bond restraints: 23399
  Sorted by residual:
  bond pdb=" C   TRP F   3 "
       pdb=" O   TRP F   3 "
    ideal  model  delta    sigma   weight residual
    1.234  1.396 -0.162 1.23e-02 6.61e+03 1.74e+02
  bond pdb=" CZ3 TRP F   3 "
       pdb=" HZ3 TRP F   3 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" CD1 TRP F   7 "
       pdb=" HD1 TRP F   7 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.64e+01
  bond pdb=" CE3 TRP F   3 "
       pdb=" HE3 TRP F   3 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.64e+01
  bond pdb=" CZ2 TRP F   3 "
       pdb=" HZ2 TRP F   3 "
    ideal  model  delta    sigma   weight residual
    0.930  1.080 -0.150 2.00e-02 2.50e+03 5.63e+01
  ... (remaining 23394 not shown)

  Histogram of bond angle deviations from ideal:
       91.56 -   100.07: 5
      100.07 -   108.57: 7168
      108.57 -   117.07: 22945
      117.07 -   125.58: 11660
      125.58 -   134.08: 296
  Bond angle restraints: 42074
  Sorted by residual:
  angle pdb=" CE2 0AF F   1 "
        pdb=" CZ2 0AF F   1 "
        pdb=" O1  0AF F   1 "
      ideal   model   delta    sigma   weight residual
     123.82  105.58   18.24 3.00e+00 1.11e-01 3.70e+01
  angle pdb=" CH2 0AF F   1 "
        pdb=" CZ2 0AF F   1 "
        pdb=" O1  0AF F   1 "
      ideal   model   delta    sigma   weight residual
     118.70  100.51   18.19 3.00e+00 1.11e-01 3.68e+01
  angle pdb=" CA  LYS F   5 "
        pdb=" CB  LYS F   5 "
        pdb=" HB3 LYS F   5 "
      ideal   model   delta    sigma   weight residual
     109.00   91.58   17.42 3.00e+00 1.11e-01 3.37e+01
  angle pdb=" CA  TRP F   3 "
        pdb=" C   TRP F   3 "
        pdb=" O   TRP F   3 "
      ideal   model   delta    sigma   weight residual
     121.36  114.66    6.70 1.20e+00 6.94e-01 3.12e+01
  angle pdb=" CG  LYS F   5 "
        pdb=" CB  LYS F   5 "
        pdb=" HB3 LYS F   5 "
      ideal   model   delta    sigma   weight residual
     108.00   91.56   16.44 3.00e+00 1.11e-01 3.00e+01
  ... (remaining 42069 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 9898
       17.86 -    35.73: 691
       35.73 -    53.59: 148
       53.59 -    71.46: 25
       71.46 -    89.32: 12
  Dihedral angle restraints: 10774
    sinusoidal: 5656
      harmonic: 5118
  Sorted by residual:
  dihedral pdb=" CB  CYS A 690 "
           pdb=" SG  CYS A 690 "
           pdb=" SG  CYS A 700 "
           pdb=" CB  CYS A 700 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -130.57   44.57     1      1.00e+01 1.00e-02 2.76e+01
  dihedral pdb=" CA  TRP A 546 "
           pdb=" C   TRP A 546 "
           pdb=" N   ARG A 547 "
           pdb=" CA  ARG A 547 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.79   22.21     0      5.00e+00 4.00e-02 1.97e+01
  dihedral pdb=" CA  SER A 425 "
           pdb=" C   SER A 425 "
           pdb=" N   PHE A 426 "
           pdb=" CA  PHE A 426 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.02   20.98     0      5.00e+00 4.00e-02 1.76e+01
  ... (remaining 10771 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1094
       0.030 -    0.061: 471
       0.061 -    0.091: 92
       0.091 -    0.121: 103
       0.121 -    0.151: 20
  Chirality restraints: 1780
  Sorted by residual:
  chirality pdb=" CA  VAL B 247 "
            pdb=" N   VAL B 247 "
            pdb=" C   VAL B 247 "
            pdb=" CB  VAL B 247 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.74e-01
  chirality pdb=" CA  ILE B 164 "
            pdb=" N   ILE B 164 "
            pdb=" C   ILE B 164 "
            pdb=" CB  ILE B 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.16e-01
  chirality pdb=" CA  ILE B 296 "
            pdb=" N   ILE B 296 "
            pdb=" C   ILE B 296 "
            pdb=" CB  ILE B 296 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.79e-01
  ... (remaining 1777 not shown)

  Planarity restraints: 3589
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  0AF F   1 "    0.257 2.00e-02 2.50e+03   3.06e-01 2.57e+03
        pdb=" CG  0AF F   1 "    0.052 2.00e-02 2.50e+03
        pdb=" CD1 0AF F   1 "   -0.093 2.00e-02 2.50e+03
        pdb=" CD2 0AF F   1 "   -0.018 2.00e-02 2.50e+03
        pdb=" NE1 0AF F   1 "   -0.252 2.00e-02 2.50e+03
        pdb=" CE2 0AF F   1 "   -0.209 2.00e-02 2.50e+03
        pdb=" CE3 0AF F   1 "    0.059 2.00e-02 2.50e+03
        pdb=" CZ2 0AF F   1 "   -0.321 2.00e-02 2.50e+03
        pdb=" CZ3 0AF F   1 "   -0.054 2.00e-02 2.50e+03
        pdb=" CH2 0AF F   1 "   -0.242 2.00e-02 2.50e+03
        pdb=" O1  0AF F   1 "    0.823 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 546 "   -0.025 2.00e-02 2.50e+03   1.64e-02 1.07e+01
        pdb=" CG  TRP A 546 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 546 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 546 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 546 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 546 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 546 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 546 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 546 "   -0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 546 "   -0.007 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 546 "   -0.010 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 546 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 546 "    0.007 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 546 "    0.000 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 546 "   -0.004 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 546 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 154 "    0.029 5.00e-02 4.00e+02   4.31e-02 2.98e+00
        pdb=" N   PRO B 155 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B 155 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 155 "    0.024 5.00e-02 4.00e+02
  ... (remaining 3586 not shown)

  Histogram of nonbonded interaction distances:
        1.27 -     1.93: 82
        1.93 -     2.60: 25723
        2.60 -     3.27: 66718
        3.27 -     3.93: 85387
        3.93 -     4.60: 134760
  Nonbonded interactions: 312670
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 520 "
            pdb="HD21 ASN A 520 "
     model   vdw
     1.267 1.850
  nonbonded pdb=" CH2 TRP F   3 "
            pdb=" CB  LYS F   5 "
     model   vdw
     1.491 3.450
  nonbonded pdb=" O   MET A 545 "
            pdb=" H   TYR A 548 "
     model   vdw
     1.547 1.850
  nonbonded pdb=" HD1 HIS A 533 "
            pdb=" OD1 ASP A 568 "
     model   vdw
     1.606 1.850
  nonbonded pdb=" HG  SER A 502 "
            pdb=" OE1 GLN A 542 "
     model   vdw
     1.615 1.850
  ... (remaining 312665 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.470
  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:             0.400
  Extract box with map and model:          11.110
  Check model and map are aligned:         0.320
  Set scattering table:                    0.220
  Process input model:                     74.460
  Find NCS groups from input model:        0.420
  Set up NCS constraints:                  0.070
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   94.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
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   0.162  12046  Z= 0.195
  Angle     :  0.519  18.244  16372  Z= 0.274
  Chirality :  0.042   0.151   1780
  Planarity :  0.007   0.306   2155
  Dihedral  : 14.250  89.324   4360
  Min Nonbonded Distance : 1.491

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.16 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.22), residues: 1488
  helix:  2.47 (0.30), residues: 307
  sheet: -0.75 (0.23), residues: 468
  loop : -1.07 (0.23), residues: 713

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.052   0.002   TRP A 546 
   HIS   0.005   0.001   HIS D 102 
   PHE   0.008   0.001   PHE A 791 
   TYR   0.013   0.001   TYR D 184 
   ARG   0.007   0.000   ARG B 355 

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 1.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 116
  average time/residue: 0.5027
  time to fit residues: 86.7373
Evaluate side-chains
  98 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 1.796 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.2912
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 124 optimal weight:    2.9990
   chunk 111 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0980
   chunk 75 optimal weight:    0.7980
   chunk 59 optimal weight:    0.8980
   chunk 115 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 133 optimal weight:    0.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
A 520 ASN
A 731 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.0275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  12046  Z= 0.170
  Angle     :  0.440   4.796  16372  Z= 0.233
  Chirality :  0.042   0.150   1780
  Planarity :  0.003   0.043   2155
  Dihedral  :  4.012  20.801   1650
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  3.25 %
    Favored  : 95.88 %
  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 (0.22), residues: 1488
  helix:  2.47 (0.30), residues: 310
  sheet: -0.71 (0.23), residues: 469
  loop : -1.02 (0.23), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.019   0.001   TRP A 546 
   HIS   0.009   0.001   HIS D 102 
   PHE   0.008   0.001   PHE A 517 
   TYR   0.014   0.001   TYR D 184 
   ARG   0.002   0.000   ARG B 355 

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 1.973 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 11
  outliers final: 10
  residues processed: 101
  average time/residue: 0.5226
  time to fit residues: 77.7562
Evaluate side-chains
  103 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 1.832 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.2603
  time to fit residues: 7.4357
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 111 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 133 optimal weight:    1.9990
   chunk 144 optimal weight:    0.9990
   chunk 119 optimal weight:    0.0870
   chunk 132 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0270
   chunk 107 optimal weight:    1.9990
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
A 520 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.0433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020  12046  Z= 0.135
  Angle     :  0.419   4.599  16372  Z= 0.222
  Chirality :  0.042   0.144   1780
  Planarity :  0.003   0.044   2155
  Dihedral  :  3.872  20.005   1650
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  4.52 %
    Favored  : 95.32 %
  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: -0.17 (0.22), residues: 1488
  helix:  2.62 (0.30), residues: 309
  sheet: -0.68 (0.23), residues: 472
  loop : -0.91 (0.23), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.001   TRP A 546 
   HIS   0.007   0.001   HIS D 102 
   PHE   0.007   0.001   PHE A 426 
   TYR   0.013   0.001   TYR D 184 
   ARG   0.001   0.000   ARG B 355 

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 102
  time to evaluate  : 1.829 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 104
  average time/residue: 0.5549
  time to fit residues: 83.1403
Evaluate side-chains
  97 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 1.789 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.3809
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 132 optimal weight:    0.9990
   chunk 100 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 134 optimal weight:    1.9990
   chunk 142 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 127 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 520 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.0531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  12046  Z= 0.227
  Angle     :  0.449   4.969  16372  Z= 0.238
  Chirality :  0.042   0.157   1780
  Planarity :  0.003   0.048   2155
  Dihedral  :  3.965  20.158   1650
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  5.86 %
    Favored  : 93.58 %
  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: -0.28 (0.22), residues: 1488
  helix:  2.50 (0.30), residues: 310
  sheet: -0.76 (0.23), residues: 482
  loop : -0.95 (0.23), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP A 546 
   HIS   0.005   0.001   HIS D 102 
   PHE   0.011   0.001   PHE A 791 
   TYR   0.014   0.001   TYR D 184 
   ARG   0.005   0.000   ARG A 237 

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 1.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 6
  residues processed: 100
  average time/residue: 0.5389
  time to fit residues: 77.8598
Evaluate side-chains
  102 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 1.881 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.2603
  time to fit residues: 5.2118
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 118 optimal weight:    5.9990
   chunk 80 optimal weight:    0.5980
   chunk 2 optimal weight:    4.9990
   chunk 105 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 121 optimal weight:    5.9990
   chunk 98 optimal weight:    0.9980
   chunk 0 optimal weight:   30.0000
   chunk 72 optimal weight:    1.9990
   chunk 127 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 520 ASN
B 230 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.0622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  12046  Z= 0.239
  Angle     :  0.452   5.043  16372  Z= 0.241
  Chirality :  0.042   0.157   1780
  Planarity :  0.003   0.049   2155
  Dihedral  :  4.017  20.655   1650
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  6.97 %
    Favored  : 92.71 %
  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: -0.29 (0.22), residues: 1488
  helix:  2.44 (0.30), residues: 310
  sheet: -0.74 (0.23), residues: 476
  loop : -0.96 (0.23), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP B 348 
   HIS   0.005   0.001   HIS D 102 
   PHE   0.010   0.001   PHE A 791 
   TYR   0.013   0.001   TYR D 184 
   ARG   0.006   0.000   ARG B 355 

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 1.703 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 2
  residues processed: 100
  average time/residue: 0.5376
  time to fit residues: 78.1807
Evaluate side-chains
  97 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 1.811 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.3710
  time to fit residues: 3.5508
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 127 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 142 optimal weight:    0.8980
   chunk 118 optimal weight:    5.9990
   chunk 65 optimal weight:    0.7980
   chunk 11 optimal weight:    4.9990
   chunk 74 optimal weight:    0.7980
   chunk 137 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 520 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.0681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  12046  Z= 0.175
  Angle     :  0.432   4.761  16372  Z= 0.229
  Chirality :  0.042   0.150   1780
  Planarity :  0.003   0.048   2155
  Dihedral  :  3.918  20.701   1650
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  7.92 %
    Favored  : 91.44 %
  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: -0.19 (0.22), residues: 1488
  helix:  2.51 (0.30), residues: 310
  sheet: -0.68 (0.23), residues: 472
  loop : -0.89 (0.23), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP B 348 
   HIS   0.004   0.001   HIS D 102 
   PHE   0.009   0.001   PHE A 517 
   TYR   0.013   0.001   TYR D 184 
   ARG   0.005   0.000   ARG B 355 

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 1.908 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 7
  residues processed: 97
  average time/residue: 0.5321
  time to fit residues: 75.3728
Evaluate side-chains
  100 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 1.770 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.2542
  time to fit residues: 5.5307
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 81 optimal weight:    0.0670
   chunk 103 optimal weight:    4.9990
   chunk 80 optimal weight:    0.0980
   chunk 119 optimal weight:    0.0370
   chunk 79 optimal weight:    0.8980
   chunk 141 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.3996

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

Flipped N/Q/H residues before XYZ refinement:
A 520 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.0768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019  12046  Z= 0.120
  Angle     :  0.414   4.449  16372  Z= 0.218
  Chirality :  0.041   0.141   1780
  Planarity :  0.003   0.047   2155
  Dihedral  :  3.761  19.950   1650
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  8.32 %
    Favored  : 91.52 %
  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: -0.01 (0.22), residues: 1488
  helix:  2.63 (0.30), residues: 316
  sheet: -0.56 (0.23), residues: 467
  loop : -0.81 (0.23), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP B 348 
   HIS   0.004   0.001   HIS D 102 
   PHE   0.007   0.001   PHE A 517 
   TYR   0.013   0.001   TYR D 184 
   ARG   0.005   0.000   ARG B 355 

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 98
  time to evaluate  : 1.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 100
  average time/residue: 0.5363
  time to fit residues: 78.5726
Evaluate side-chains
  97 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 1.934 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.5273
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 84 optimal weight:    0.2980
   chunk 42 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 111 optimal weight:    0.8980
   chunk 128 optimal weight:    1.9990
   chunk 135 optimal weight:    0.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
A 520 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.0796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  12046  Z= 0.167
  Angle     :  0.426   4.612  16372  Z= 0.225
  Chirality :  0.042   0.147   1780
  Planarity :  0.003   0.046   2155
  Dihedral  :  3.786  19.759   1650
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  8.80 %
    Favored  : 90.73 %
  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 (0.22), residues: 1488
  helix:  2.63 (0.30), residues: 316
  sheet: -0.58 (0.23), residues: 472
  loop : -0.79 (0.23), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP B 348 
   HIS   0.004   0.001   HIS D 102 
   PHE   0.008   0.001   PHE A 791 
   TYR   0.014   0.001   TYR D 184 
   ARG   0.006   0.000   ARG B 355 

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 2.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 4
  residues processed: 101
  average time/residue: 0.5382
  time to fit residues: 80.0734
Evaluate side-chains
  102 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 1.762 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.2698
  time to fit residues: 4.2583
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 123 optimal weight:    5.9990
   chunk 132 optimal weight:    1.9990
   chunk 135 optimal weight:    0.9990
   chunk 79 optimal weight:    0.0870
   chunk 57 optimal weight:    0.9980
   chunk 103 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 119 optimal weight:    0.0980
   chunk 124 optimal weight:    1.9990
   chunk 131 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   overall best weight:    0.6160

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

Flipped N/Q/H residues before XYZ refinement:
A 520 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.0848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020  12046  Z= 0.140
  Angle     :  0.418   4.427  16372  Z= 0.220
  Chirality :  0.041   0.141   1780
  Planarity :  0.003   0.047   2155
  Dihedral  :  3.726  19.711   1650
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  8.95 %
    Favored  : 90.89 %
  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:  0.08 (0.22), residues: 1488
  helix:  2.73 (0.30), residues: 315
  sheet: -0.52 (0.23), residues: 472
  loop : -0.74 (0.23), residues: 701

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP B 348 
   HIS   0.004   0.001   HIS D 102 
   PHE   0.008   0.001   PHE A 517 
   TYR   0.013   0.001   TYR D 184 
   ARG   0.007   0.000   ARG B 355 

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 96
  time to evaluate  : 1.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 98
  average time/residue: 0.5453
  time to fit residues: 78.7850
Evaluate side-chains
  97 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 1.806 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.2485
  time to fit residues: 2.6843
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 139 optimal weight:    0.1980
   chunk 85 optimal weight:    2.9990
   chunk 66 optimal weight:    6.9990
   chunk 97 optimal weight:    0.9980
   chunk 146 optimal weight:    1.9990
   chunk 134 optimal weight:    0.9980
   chunk 116 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 92 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 520 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.0865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021  12046  Z= 0.163
  Angle     :  0.423   4.492  16372  Z= 0.223
  Chirality :  0.041   0.145   1780
  Planarity :  0.003   0.046   2155
  Dihedral  :  3.734  19.731   1650
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  9.51 %
    Favored  : 90.41 %
  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:  0.05 (0.22), residues: 1488
  helix:  2.70 (0.30), residues: 316
  sheet: -0.55 (0.23), residues: 473
  loop : -0.76 (0.23), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP B 348 
   HIS   0.004   0.001   HIS D 102 
   PHE   0.008   0.001   PHE A 517 
   TYR   0.013   0.001   TYR D 184 
   ARG   0.007   0.000   ARG B 355 

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 1.824 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 97
  average time/residue: 0.5428
  time to fit residues: 76.9075
Evaluate side-chains
  97 residues out of total 1262 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 1.798 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.3238
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 124 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 107 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 116 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 119 optimal weight:    0.1980
   chunk 14 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 102 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 520 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.176410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.160953 restraints weight = 34377.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 0.76
r_work: 0.3200 rms_B_bonded: 0.90 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 1.67 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.0889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  12046  Z= 0.161
  Angle     :  0.424   4.457  16372  Z= 0.224
  Chirality :  0.042   0.144   1780
  Planarity :  0.003   0.047   2155
  Dihedral  :  3.739  19.781   1650
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  9.51 %
    Favored  : 90.33 %
  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:  0.05 (0.22), residues: 1488
  helix:  2.71 (0.30), residues: 316
  sheet: -0.55 (0.23), residues: 467
  loop : -0.76 (0.23), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP B 348 
   HIS   0.004   0.001   HIS D 102 
   PHE   0.008   0.001   PHE A 517 
   TYR   0.013   0.001   TYR D 184 
   ARG   0.008   0.000   ARG B 355 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4798.58 seconds
wall clock time: 86 minutes 0.59 seconds (5160.59 seconds total)