Starting phenix.real_space_refine
on Fri Dec  8 02:41:52 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf8_25077/12_2023/7sf8_25077_neut.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf8_25077/12_2023/7sf8_25077.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf8_25077/12_2023/7sf8_25077.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf8_25077/12_2023/7sf8_25077.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf8_25077/12_2023/7sf8_25077_neut.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf8_25077/12_2023/7sf8_25077_neut.pdb"
  }
  resolution = 2.7
  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=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      45      5.16       5
     C    4266      2.51       5
     N    1111      2.21       5
     O    1239      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  394": "OE1" <-> "OE2"
    Residue "A GLU  490": "OE1" <-> "OE2"
    Residue "A ARG  559": "NH1" <-> "NH2"
    Residue "A PHE  629": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  649": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 6661
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1993
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 1993
          Classifications: {'peptide': 257}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 6, 'TRANS': 250}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 52
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 4, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "B"
      Number of atoms: 1708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1708
          Classifications: {'peptide': 212}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 3, 'TRANS': 208}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 50
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 5, 'TRP:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 45
    Chain: "C"
      Number of atoms: 2582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2582
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "D"
      Number of atoms: 378
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 378
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 15
  Time building chain proxies: 4.55, per 1000 atoms: 0.68
  Number of scatterers: 6661
  At special positions: 0
  Unit cell: (102.389, 93.7116, 118.007, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      45     16.00
     O    1239      8.00
     N    1111      7.00
     C    4266      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 469 " - pdb=" SG  CYS A 556 " distance=2.09

  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: 2.19
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1624

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 9 sheets defined
      42.3% alpha, 19.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 384 through 388
      removed outlier: 3.625A  pdb=" N   VAL A 387 " --> pdb=" O   TYR A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 427
      removed outlier: 3.640A  pdb=" N   HIS A 401 " --> pdb=" O   ALA A 397 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   TYR A 402 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 464
      removed outlier: 3.901A  pdb=" N   LYS A 438 " --> pdb=" O   ASP A 434 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU A 456 " --> pdb=" O   THR A 452 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   SER A 457 " --> pdb=" O   SER A 453 " (cutoff:3.500A)
      removed outlier: 4.794A  pdb=" N   GLU A 458 " --> pdb=" O   PHE A 454 " (cutoff:3.500A)
      Proline residue:  A 459  - end of helix
      removed outlier: 3.580A  pdb=" N   LEU A 462 " --> pdb=" O   GLU A 458 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   THR A 463 " --> pdb=" O   PRO A 459 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   GLY A 464 " --> pdb=" O   VAL A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 499
      removed outlier: 4.173A  pdb=" N   ALA A 473 " --> pdb=" O   CYS A 469 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ILE A 474 " --> pdb=" O   ARG A 470 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   CYS A 483 " --> pdb=" O   SER A 479 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   SER A 485 " --> pdb=" O   LEU A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 529
      removed outlier: 3.585A  pdb=" N   MET A 516 " --> pdb=" O   LYS A 512 " (cutoff:3.500A)
      Proline residue:  A 521  - end of helix
    Processing helix  chain 'A' and resid 532 through 534
      No H-bonds generated for 'chain 'A' and resid 532 through 534'
    Processing helix  chain 'A' and resid 560 through 568
      removed outlier: 4.043A  pdb=" N   SER A 564 " --> pdb=" O   ASP A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 591
    Processing helix  chain 'A' and resid 602 through 614
    Processing helix  chain 'A' and resid 615 through 625
      removed outlier: 4.055A  pdb=" N   PHE A 624 " --> pdb=" O   PHE A 621 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 643
      removed outlier: 3.518A  pdb=" N   VAL A 633 " --> pdb=" O   PHE A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 656
    Processing helix  chain 'B' and resid 12 through 26
      removed outlier: 3.579A  pdb=" N   SER B  16 " --> pdb=" O   ALA B  12 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   GLU B  26 " --> pdb=" O   CYS B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 32
      removed outlier: 3.679A  pdb=" N   VAL B  30 " --> pdb=" O   GLU B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 52
    Processing helix  chain 'B' and resid 117 through 130
      removed outlier: 3.607A  pdb=" N   SER B 121 " --> pdb=" O   ARG B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 153
    Processing helix  chain 'B' and resid 157 through 161
    Processing helix  chain 'B' and resid 171 through 185
    Processing helix  chain 'B' and resid 206 through 228
      removed outlier: 3.708A  pdb=" N   ASP B 222 " --> pdb=" O   THR B 218 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLN B 226 " --> pdb=" O   ASP B 222 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU B 227 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 25
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'D' and resid 10 through 24
      removed outlier: 3.540A  pdb=" N   ASN D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
    Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 537
    Processing sheet with id=AA2, first strand: chain 'B' and resid 69 through 75
      removed outlier: 3.552A  pdb=" N   VAL B  34 " --> pdb=" O   PRO B  80 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   VAL B  86 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   LYS B  35 " --> pdb=" O   SER B 105 " (cutoff:3.500A)
      removed outlier: 7.878A  pdb=" N   LEU B 107 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   LEU B  37 " --> pdb=" O   LEU B 107 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   LEU B 109 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   LEU B  39 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   ILE B 106 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   PHE B 142 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   PHE B 108 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 51
      removed outlier: 6.755A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   CYS C 317 " --> pdb=" O   GLY C 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63
      removed outlier: 4.057A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU C  70 " --> pdb=" O   TRP C  82 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   SER C  74 " --> pdb=" O   LYS C  78 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.716A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 5.084A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.242A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   CYS C 121 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   GLU C 138 " --> pdb=" O   CYS C 121 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   ILE C 123 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ARG C 134 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151
      removed outlier: 6.751A  pdb=" N   SER C 160 " --> pdb=" O   SER C 147 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   CYS C 149 " --> pdb=" O   VAL C 158 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   VAL C 158 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 5.225A  pdb=" N   PHE C 151 " --> pdb=" O   GLN C 156 " (cutoff:3.500A)
      removed outlier: 7.681A  pdb=" N   GLN C 156 " --> pdb=" O   PHE C 151 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ILE C 157 " --> pdb=" O   TRP C 169 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   THR C 178 " --> pdb=" O   LEU C 168 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192
      removed outlier: 6.787A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.161A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   PHE C 199 " --> pdb=" O   TRP C 211 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   SER C 207 " --> pdb=" O   ALA C 203 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.842A  pdb=" N   GLY C 244 " --> pdb=" O   ASN C 230 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   ILE C 232 " --> pdb=" O   ALA C 242 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ALA C 242 " --> pdb=" O   ILE C 232 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   PHE C 234 " --> pdb=" O   ALA C 240 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   ALA C 240 " --> pdb=" O   PHE C 234 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   MET C 262 " --> pdb=" O   LEU C 252 " (cutoff:3.500A)
      removed outlier: 6.091A  pdb=" N   ASP C 254 " --> pdb=" O   GLU C 260 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   GLU C 260 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.785A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   GLY C 306 " --> pdb=" O   VAL C 296 " (cutoff:3.500A)
      removed outlier: 5.721A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)

    313 hydrogen bonds defined for protein.
    891 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.80

  Time building geometry restraints manager: 2.44 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1784
        1.33 -     1.46: 1405
        1.46 -     1.58: 3538
        1.58 -     1.70: 0
        1.70 -     1.83: 65
  Bond restraints: 6792
  Sorted by residual:
  bond pdb=" CA  SER A 465 "
       pdb=" CB  SER A 465 "
    ideal  model  delta    sigma   weight residual
    1.530  1.454  0.076 1.43e-02 4.89e+03 2.80e+01
  bond pdb=" CA  SER A 564 "
       pdb=" CB  SER A 564 "
    ideal  model  delta    sigma   weight residual
    1.529  1.463  0.066 1.55e-02 4.16e+03 1.83e+01
  bond pdb=" CA  SER A 472 "
       pdb=" CB  SER A 472 "
    ideal  model  delta    sigma   weight residual
    1.528  1.461  0.067 1.59e-02 3.96e+03 1.78e+01
  bond pdb=" CA  SER A 561 "
       pdb=" CB  SER A 561 "
    ideal  model  delta    sigma   weight residual
    1.531  1.468  0.063 1.56e-02 4.11e+03 1.63e+01
  bond pdb=" N   ILE A 558 "
       pdb=" CA  ILE A 558 "
    ideal  model  delta    sigma   weight residual
    1.458  1.506 -0.048 1.20e-02 6.94e+03 1.57e+01
  ... (remaining 6787 not shown)

  Histogram of bond angle deviations from ideal:
       98.69 -   105.77: 80
      105.77 -   112.84: 3688
      112.84 -   119.92: 2296
      119.92 -   126.99: 3080
      126.99 -   134.07: 72
  Bond angle restraints: 9216
  Sorted by residual:
  angle pdb=" N   ARG A 470 "
        pdb=" CA  ARG A 470 "
        pdb=" C   ARG A 470 "
      ideal   model   delta    sigma   weight residual
     113.50  106.46    7.04 1.23e+00 6.61e-01 3.27e+01
  angle pdb=" N   GLN B 226 "
        pdb=" CA  GLN B 226 "
        pdb=" C   GLN B 226 "
      ideal   model   delta    sigma   weight residual
     113.12  106.97    6.15 1.25e+00 6.40e-01 2.42e+01
  angle pdb=" N   LEU A 481 "
        pdb=" CA  LEU A 481 "
        pdb=" C   LEU A 481 "
      ideal   model   delta    sigma   weight residual
     113.18  107.56    5.62 1.21e+00 6.83e-01 2.16e+01
  angle pdb=" N   ALA A 467 "
        pdb=" CA  ALA A 467 "
        pdb=" CB  ALA A 467 "
      ideal   model   delta    sigma   weight residual
     110.59  105.33    5.26 1.33e+00 5.65e-01 1.57e+01
  angle pdb=" N   MET A 655 "
        pdb=" CA  MET A 655 "
        pdb=" C   MET A 655 "
      ideal   model   delta    sigma   weight residual
     111.36  107.22    4.14 1.09e+00 8.42e-01 1.44e+01
  ... (remaining 9211 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.21: 3644
       17.21 -    34.43: 307
       34.43 -    51.64: 51
       51.64 -    68.85: 5
       68.85 -    86.06: 4
  Dihedral angle restraints: 4011
    sinusoidal: 1508
      harmonic: 2503
  Sorted by residual:
  dihedral pdb=" CA  ASP C 258 "
           pdb=" C   ASP C 258 "
           pdb=" N   GLN C 259 "
           pdb=" CA  GLN C 259 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.32   20.68     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  VAL A 531 "
           pdb=" C   VAL A 531 "
           pdb=" N   ASP A 532 "
           pdb=" CA  ASP A 532 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.53   20.47     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  ARG A 429 "
           pdb=" C   ARG A 429 "
           pdb=" N   ARG A 430 "
           pdb=" CA  ARG A 430 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.54  -18.46     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 4008 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 860
       0.056 -    0.113: 174
       0.113 -    0.169: 38
       0.169 -    0.226: 5
       0.226 -    0.282: 2
  Chirality restraints: 1079
  Sorted by residual:
  chirality pdb=" CA  TYR A 536 "
            pdb=" N   TYR A 536 "
            pdb=" C   TYR A 536 "
            pdb=" CB  TYR A 536 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.99e+00
  chirality pdb=" CA  ILE A 540 "
            pdb=" N   ILE A 540 "
            pdb=" C   ILE A 540 "
            pdb=" CB  ILE A 540 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CA  ARG A 470 "
            pdb=" N   ARG A 470 "
            pdb=" C   ARG A 470 "
            pdb=" CB  ARG A 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 1076 not shown)

  Planarity restraints: 1160
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 469 "    0.015 2.00e-02 2.50e+03   3.05e-02 9.28e+00
        pdb=" C   CYS A 469 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   CYS A 469 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ARG A 470 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 558 "   -0.012 2.00e-02 2.50e+03   2.51e-02 6.32e+00
        pdb=" C   ILE A 558 "    0.043 2.00e-02 2.50e+03
        pdb=" O   ILE A 558 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ARG A 559 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 557 "    0.011 2.00e-02 2.50e+03   2.20e-02 4.82e+00
        pdb=" C   TRP A 557 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   TRP A 557 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ILE A 558 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1157 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1607
        2.80 -     3.32: 5912
        3.32 -     3.85: 10104
        3.85 -     4.37: 12052
        4.37 -     4.90: 21621
  Nonbonded interactions: 51296
  Sorted by model distance:
  nonbonded pdb=" NE1 TRP A 617 "
            pdb=" OE1 GLN A 644 "
     model   vdw
     2.270 2.520
  nonbonded pdb=" O   TYR A 505 "
            pdb=" NH2 ARG B  32 "
     model   vdw
     2.298 2.520
  nonbonded pdb=" O   GLY B  40 "
            pdb=" NH2 ARG B  90 "
     model   vdw
     2.371 2.520
  nonbonded pdb=" O   VAL A 563 "
            pdb=" OG1 THR A 567 "
     model   vdw
     2.387 2.440
  nonbonded pdb=" O   ASP C 228 "
            pdb=" OG  SER C 245 "
     model   vdw
     2.397 2.440
  ... (remaining 51291 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:             4.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          9.570
  Check model and map are aligned:         0.100
  Set scattering table:                    0.060
  Process input model:                     21.690
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
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      :  0.005   0.076   6792  Z= 0.347
  Angle     :  0.740   7.037   9216  Z= 0.475
  Chirality :  0.050   0.282   1079
  Planarity :  0.004   0.054   1160
  Dihedral  : 13.034  86.064   2384
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.97 %
    Favored  : 98.89 %
  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:  0.40 (0.30), residues: 846
  helix:  1.57 (0.30), residues: 341
  sheet:  0.81 (0.41), residues: 161
  loop : -1.40 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP C  82 
   HIS   0.004   0.001   HIS B 221 
   PHE   0.021   0.002   PHE A 649 
   TYR   0.014   0.002   TYR A 408 
   ARG   0.006   0.000   ARG A 559 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 140
  time to evaluate  : 0.792 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 141
  average time/residue: 1.3123
  time to fit residues: 193.6600
Evaluate side-chains
  112 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 111
  time to evaluate  : 0.732 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 1
  residues processed: 0
  time to fit residues: 1.0160
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 42 optimal weight:    0.1980
   chunk 34 optimal weight:    0.2980
   chunk 65 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0770
   chunk 76 optimal weight:    3.9990
   overall best weight:    0.3938

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

Flipped N/Q/H residues before XYZ refinement:
** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 268 ASN
C 293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6792  Z= 0.204
  Angle     :  0.515   5.394   9216  Z= 0.278
  Chirality :  0.042   0.133   1079
  Planarity :  0.004   0.052   1160
  Dihedral  :  4.118  18.889    915
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 10.29 %
    Favored  : 87.90 %
  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:  0.85 (0.30), residues: 846
  helix:  1.94 (0.30), residues: 348
  sheet:  1.06 (0.41), residues: 171
  loop : -1.29 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP A 486 
   HIS   0.005   0.001   HIS A 401 
   PHE   0.020   0.001   PHE A 649 
   TYR   0.011   0.001   TYR A 408 
   ARG   0.006   0.000   ARG A 496 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 0.766 
Fit side-chains
  outliers start: 13
  outliers final: 4
  residues processed: 137
  average time/residue: 1.1789
  time to fit residues: 170.2672
Evaluate side-chains
  114 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 110
  time to evaluate  : 0.747 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 2
  residues processed: 2
  average time/residue: 0.1371
  time to fit residues: 1.3942
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 63 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 21 optimal weight:    0.2980
   chunk 76 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 26 optimal weight:    0.3980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
C 268 ASN
C 293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6792  Z= 0.266
  Angle     :  0.533   6.293   9216  Z= 0.287
  Chirality :  0.043   0.138   1079
  Planarity :  0.004   0.052   1160
  Dihedral  :  4.184  17.459    915
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.80 %
    Favored  : 85.12 %
  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:  0.83 (0.30), residues: 846
  helix:  1.97 (0.30), residues: 349
  sheet:  0.98 (0.40), residues: 173
  loop : -1.34 (0.33), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.002   TRP C  82 
   HIS   0.005   0.001   HIS B 221 
   PHE   0.025   0.002   PHE A 649 
   TYR   0.011   0.001   TYR A 408 
   ARG   0.004   0.000   ARG A 496 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.729 
Fit side-chains
  outliers start: 15
  outliers final: 8
  residues processed: 128
  average time/residue: 1.2073
  time to fit residues: 162.3722
Evaluate side-chains
  117 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 0.741 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 6
  residues processed: 3
  average time/residue: 0.1043
  time to fit residues: 1.4563
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9980
   chunk 40 optimal weight:    0.5980
   chunk 72 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
C  35 ASN
C 268 ASN
C 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   6792  Z= 0.329
  Angle     :  0.562   7.286   9216  Z= 0.300
  Chirality :  0.044   0.145   1079
  Planarity :  0.004   0.053   1160
  Dihedral  :  4.262  17.001    915
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 14.33 %
    Favored  : 83.03 %
  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:  0.80 (0.30), residues: 846
  helix:  1.97 (0.30), residues: 349
  sheet:  0.94 (0.41), residues: 166
  loop : -1.33 (0.32), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.002   TRP C  82 
   HIS   0.006   0.001   HIS A 401 
   PHE   0.027   0.002   PHE A 649 
   TYR   0.011   0.001   TYR A 408 
   ARG   0.004   0.000   ARG C  96 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.735 
Fit side-chains
  outliers start: 19
  outliers final: 10
  residues processed: 117
  average time/residue: 1.3908
  time to fit residues: 170.1199
Evaluate side-chains
  117 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.789 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 5
  residues processed: 6
  average time/residue: 0.4541
  time to fit residues: 4.0653
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 46 optimal weight:    0.0470
   chunk 1 optimal weight:    0.0020
   chunk 60 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 56 optimal weight:    0.6980
   chunk 0 optimal weight:    0.3980
   chunk 41 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.3486

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

Flipped N/Q/H residues before XYZ refinement:
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  35 ASN
C 268 ASN
C 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6792  Z= 0.177
  Angle     :  0.486   6.111   9216  Z= 0.261
  Chirality :  0.041   0.138   1079
  Planarity :  0.003   0.049   1160
  Dihedral  :  4.016  24.359    915
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 15.72 %
    Favored  : 82.20 %
  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:  1.02 (0.30), residues: 846
  helix:  2.25 (0.30), residues: 349
  sheet:  0.95 (0.42), residues: 166
  loop : -1.26 (0.32), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP A 486 
   HIS   0.003   0.001   HIS A 401 
   PHE   0.021   0.001   PHE A 649 
   TYR   0.009   0.001   TYR A 408 
   ARG   0.006   0.000   ARG A 496 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.791 
Fit side-chains
  outliers start: 15
  outliers final: 8
  residues processed: 121
  average time/residue: 1.3012
  time to fit residues: 165.0399
Evaluate side-chains
  115 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.713 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 6
  residues processed: 3
  average time/residue: 0.6634
  time to fit residues: 3.1261
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    0.0070
   chunk 73 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 26 optimal weight:    0.1980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 259 GLN
C 268 ASN
C 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.3030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6792  Z= 0.217
  Angle     :  0.499   6.108   9216  Z= 0.267
  Chirality :  0.042   0.138   1079
  Planarity :  0.004   0.050   1160
  Dihedral  :  3.975  23.746    915
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 17.11 %
    Favored  : 80.81 %
  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:  1.05 (0.30), residues: 846
  helix:  2.32 (0.30), residues: 349
  sheet:  0.87 (0.41), residues: 168
  loop : -1.25 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP C  82 
   HIS   0.004   0.001   HIS A 401 
   PHE   0.022   0.001   PHE A 649 
   TYR   0.023   0.001   TYR A 495 
   ARG   0.009   0.000   ARG B 213 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.752 
Fit side-chains
  outliers start: 15
  outliers final: 10
  residues processed: 122
  average time/residue: 1.1299
  time to fit residues: 144.5549
Evaluate side-chains
  116 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.510 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 9
  residues processed: 2
  average time/residue: 0.1037
  time to fit residues: 1.0187
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 46 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 268 ASN
C 293 ASN
D  59 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.3110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.071   6792  Z= 0.475
  Angle     :  0.631   8.025   9216  Z= 0.335
  Chirality :  0.048   0.162   1079
  Planarity :  0.004   0.054   1160
  Dihedral  :  4.444  22.101    915
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 17.25 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.30), residues: 846
  helix:  2.12 (0.30), residues: 339
  sheet:  0.86 (0.40), residues: 177
  loop : -1.36 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.002   TRP C  82 
   HIS   0.006   0.001   HIS A 401 
   PHE   0.031   0.002   PHE A 649 
   TYR   0.031   0.002   TYR A 495 
   ARG   0.009   0.001   ARG B 213 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.758 
Fit side-chains
  outliers start: 16
  outliers final: 12
  residues processed: 114
  average time/residue: 1.3961
  time to fit residues: 166.5078
Evaluate side-chains
  116 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.741 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 8
  residues processed: 5
  average time/residue: 0.7020
  time to fit residues: 4.8025
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 24 optimal weight:    0.2980
   chunk 15 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 7 optimal weight:    0.3980
   chunk 63 optimal weight:    0.7980
   chunk 73 optimal weight:    0.5980
   chunk 77 optimal weight:    0.6980
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  35 ASN
C 268 ASN
C 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.3147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6792  Z= 0.236
  Angle     :  0.521   6.049   9216  Z= 0.279
  Chirality :  0.042   0.133   1079
  Planarity :  0.004   0.050   1160
  Dihedral  :  4.150  28.214    915
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 16.83 %
    Favored  : 81.08 %
  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:  1.01 (0.30), residues: 846
  helix:  2.39 (0.30), residues: 340
  sheet:  0.83 (0.41), residues: 173
  loop : -1.33 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.002   TRP C  82 
   HIS   0.004   0.001   HIS A 401 
   PHE   0.023   0.001   PHE A 649 
   TYR   0.024   0.001   TYR A 495 
   ARG   0.008   0.000   ARG B 213 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.819 
Fit side-chains
  outliers start: 15
  outliers final: 12
  residues processed: 117
  average time/residue: 1.2832
  time to fit residues: 157.4547
Evaluate side-chains
  118 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.644 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 11
  residues processed: 2
  average time/residue: 0.1865
  time to fit residues: 1.3726
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 23 optimal weight:    0.4980
   chunk 68 optimal weight:    2.9990
   chunk 71 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0570
   chunk 79 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  35 ASN
C 268 ASN
C 293 ASN
C 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.3194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6792  Z= 0.273
  Angle     :  0.540   6.935   9216  Z= 0.288
  Chirality :  0.043   0.136   1079
  Planarity :  0.004   0.051   1160
  Dihedral  :  4.098  19.524    915
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.25 %
    Favored  : 80.81 %
  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:  1.00 (0.30), residues: 846
  helix:  2.39 (0.30), residues: 340
  sheet:  0.81 (0.41), residues: 173
  loop : -1.34 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.002   TRP C  82 
   HIS   0.004   0.001   HIS A 401 
   PHE   0.024   0.002   PHE A 649 
   TYR   0.024   0.001   TYR A 495 
   ARG   0.008   0.000   ARG B 213 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.809 
Fit side-chains
  outliers start: 14
  outliers final: 12
  residues processed: 116
  average time/residue: 1.3651
  time to fit residues: 165.8435
Evaluate side-chains
  117 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.775 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 11
  residues processed: 2
  average time/residue: 0.9217
  time to fit residues: 3.0674
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 83 optimal weight:    0.0010
   chunk 77 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  35 ASN
C 259 GLN
C 268 ASN
C 293 ASN
** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.3216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6792  Z= 0.266
  Angle     :  0.533   6.434   9216  Z= 0.285
  Chirality :  0.043   0.141   1079
  Planarity :  0.004   0.051   1160
  Dihedral  :  4.024  19.434    915
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.39 %
    Favored  : 80.67 %
  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:  0.94 (0.30), residues: 846
  helix:  2.28 (0.30), residues: 348
  sheet:  0.82 (0.41), residues: 173
  loop : -1.42 (0.32), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.002   TRP C  82 
   HIS   0.004   0.001   HIS A 401 
   PHE   0.024   0.001   PHE A 649 
   TYR   0.024   0.001   TYR A 495 
   ARG   0.008   0.000   ARG B 213 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.738 
Fit side-chains
  outliers start: 14
  outliers final: 12
  residues processed: 119
  average time/residue: 1.3094
  time to fit residues: 163.4106
Evaluate side-chains
  119 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.817 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 12
  residues processed: 1
  average time/residue: 0.2397
  time to fit residues: 1.4100
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 12 optimal weight:    0.1980
   chunk 58 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  35 ASN
C 268 ASN
C 293 ASN
** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.123854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.104848 restraints weight = 9660.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 1.82
r_work: 0.3361 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.3223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6792  Z= 0.259
  Angle     :  0.530   6.439   9216  Z= 0.283
  Chirality :  0.043   0.137   1079
  Planarity :  0.004   0.050   1160
  Dihedral  :  3.988  19.070    915
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 17.66 %
    Favored  : 80.11 %
  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:  0.95 (0.30), residues: 846
  helix:  2.29 (0.30), residues: 348
  sheet:  0.83 (0.41), residues: 173
  loop : -1.42 (0.32), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.002   TRP C  82 
   HIS   0.004   0.001   HIS A 401 
   PHE   0.024   0.001   PHE A 649 
   TYR   0.023   0.001   TYR A 495 
   ARG   0.008   0.000   ARG B 213 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3298.85 seconds
wall clock time: 61 minutes 31.32 seconds (3691.32 seconds total)