Starting phenix.real_space_refine
on Fri Dec  8 10:29:38 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxu_32881/12_2023/7wxu_32881_neut.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxu_32881/12_2023/7wxu_32881.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxu_32881/12_2023/7wxu_32881.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxu_32881/12_2023/7wxu_32881.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxu_32881/12_2023/7wxu_32881_neut.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxu_32881/12_2023/7wxu_32881_neut.pdb"
  }
  resolution = 2.85
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.021
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      52      5.16       5
     C    5175      2.51       5
     N    1401      2.21       5
     O    1488      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B TYR  289": "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: 8116
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1928
          Classifications: {'peptide': 234}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "R"
      Number of atoms: 2179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2179
          Classifications: {'peptide': 277}
          Link IDs: {'PTRANS': 10, 'TRANS': 266}
          Chain breaks: 1
  Time building chain proxies: 4.62, per 1000 atoms: 0.57
  Number of scatterers: 8116
  At special positions: 0
  Unit cell: (80.3, 101.2, 134.2, 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      52     16.00
     O    1488      8.00
     N    1401      7.00
     C    5175      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 657 " - pdb=" SG  CYS R 733 " distance=1.93

  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: 2.72
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1938

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 10 sheets defined
      40.7% alpha, 20.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 38
      removed outlier: 3.779A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.594A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   PHE A 238 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
      removed outlier: 3.853A  pdb=" N   ALA A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ASN A 278 " --> pdb=" O   LYS A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 283
      removed outlier: 3.550A  pdb=" N   LEU A 282 " --> pdb=" O   ASN A 279 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   ARG A 283 " --> pdb=" O   ARG A 280 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 279 through 283'
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.634A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 318
      removed outlier: 3.816A  pdb=" N   TYR A 318 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.615A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 24
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.579A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 7 through 23
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.797A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 4.061A  pdb=" N   ASN N  31 " --> pdb=" O   THR N  28 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 28 through 32'
    Processing helix  chain 'N' and resid 62 through 65
      removed outlier: 3.641A  pdb=" N   LYS N  65 " --> pdb=" O   GLY N  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 62 through 65'
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.685A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 568 through 573
      removed outlier: 3.728A  pdb=" N   ILE R 571 " --> pdb=" O   SER R 568 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   LEU R 572 " --> pdb=" O   PHE R 569 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 578 through 580
      No H-bonds generated for 'chain 'R' and resid 578 through 580'
    Processing helix  chain 'R' and resid 581 through 610
      removed outlier: 3.567A  pdb=" N   VAL R 585 " --> pdb=" O   ILE R 581 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   LYS R 586 " --> pdb=" O   PHE R 582 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   TRP R 587 " --> pdb=" O   PRO R 583 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   ILE R 588 " --> pdb=" O   VAL R 584 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   THR R 589 " --> pdb=" O   VAL R 585 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   GLY R 594 " --> pdb=" O   TYR R 590 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 611 through 614
      removed outlier: 3.725A  pdb=" N   ILE R 614 " --> pdb=" O   TRP R 611 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 611 through 614'
    Processing helix  chain 'R' and resid 617 through 646
      removed outlier: 3.532A  pdb=" N   THR R 646 " --> pdb=" O   ILE R 642 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 655 through 685
      removed outlier: 3.591A  pdb=" N   ALA R 659 " --> pdb=" O   GLY R 655 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   VAL R 661 " --> pdb=" O   CYS R 657 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 694 through 707
      removed outlier: 3.548A  pdb=" N   MET R 698 " --> pdb=" O   ALA R 694 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   TYR R 707 " --> pdb=" O   PHE R 703 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 708 through 722
    Processing helix  chain 'R' and resid 723 through 725
      No H-bonds generated for 'chain 'R' and resid 723 through 725'
    Processing helix  chain 'R' and resid 744 through 770
      Proline residue:  R 750  - end of helix
      removed outlier: 4.534A  pdb=" N   ILE R 754 " --> pdb=" O   PRO R 750 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   VAL R 755 " --> pdb=" O   ALA R 751 " (cutoff:3.500A)
      removed outlier: 5.051A  pdb=" N   VAL R 757 " --> pdb=" O   ALA R 753 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   VAL R 760 " --> pdb=" O   ALA R 756 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 785 through 801
      removed outlier: 3.728A  pdb=" N   LEU R 796 " --> pdb=" O   SER R 792 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   THR R 797 " --> pdb=" O   LEU R 793 " (cutoff:3.500A)
      Proline residue:  R 798  - end of helix
    Processing helix  chain 'R' and resid 802 through 805
    Processing helix  chain 'R' and resid 806 through 811
      removed outlier: 3.834A  pdb=" N   THR R 810 " --> pdb=" O   PHE R 806 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 821 through 829
      removed outlier: 3.943A  pdb=" N   PHE R 829 " --> pdb=" O   LEU R 825 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 829 through 838
    Processing helix  chain 'R' and resid 843 through 854
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.299A  pdb=" N   LEU A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   PHE A 222 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 8.864A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.986A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.686A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.385A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU A 291 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 7.058A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.886A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.042A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.277A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.912A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.252A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 7.160A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.400A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.904A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.960A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.959A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.024A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.892A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.768A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.252A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   SER N  49 " --> pdb=" O   TRP N  36 " (cutoff:3.500A)

    365 hydrogen bonds defined for protein.
    1038 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.23

  Time building geometry restraints manager: 3.02 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2601
        1.34 -     1.46: 1772
        1.46 -     1.58: 3836
        1.58 -     1.70: 0
        1.70 -     1.82: 74
  Bond restraints: 8283
  Sorted by residual:
  bond pdb=" N   GLN N  39 "
       pdb=" CA  GLN N  39 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.24e-02 6.50e+03 7.98e+00
  bond pdb=" N   HIS R 820 "
       pdb=" CA  HIS R 820 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.033 1.33e-02 5.65e+03 6.12e+00
  bond pdb=" N   ASN R 816 "
       pdb=" CA  ASN R 816 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.29e-02 6.01e+03 5.78e+00
  bond pdb=" N   GLN R 815 "
       pdb=" CA  GLN R 815 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.29e-02 6.01e+03 5.68e+00
  bond pdb=" N   LEU R 817 "
       pdb=" CA  LEU R 817 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.030 1.29e-02 6.01e+03 5.51e+00
  ... (remaining 8278 not shown)

  Histogram of bond angle deviations from ideal:
       99.86 -   106.73: 192
      106.73 -   113.61: 4592
      113.61 -   120.48: 3299
      120.48 -   127.35: 3054
      127.35 -   134.23: 89
  Bond angle restraints: 11226
  Sorted by residual:
  angle pdb=" N   ALA B 203 "
        pdb=" CA  ALA B 203 "
        pdb=" C   ALA B 203 "
      ideal   model   delta    sigma   weight residual
     112.03  119.60   -7.57 1.31e+00 5.83e-01 3.34e+01
  angle pdb=" N   TYR N  94 "
        pdb=" CA  TYR N  94 "
        pdb=" C   TYR N  94 "
      ideal   model   delta    sigma   weight residual
     108.90  115.35   -6.45 1.63e+00 3.76e-01 1.57e+01
  angle pdb=" C   LYS R 728 "
        pdb=" CA  LYS R 728 "
        pdb=" CB  LYS R 728 "
      ideal   model   delta    sigma   weight residual
     109.79  117.66   -7.87 2.05e+00 2.38e-01 1.47e+01
  angle pdb=" C   LEU B  55 "
        pdb=" CA  LEU B  55 "
        pdb=" CB  LEU B  55 "
      ideal   model   delta    sigma   weight residual
     109.55  103.30    6.25 1.68e+00 3.54e-01 1.38e+01
  angle pdb=" N   VAL B  90 "
        pdb=" CA  VAL B  90 "
        pdb=" C   VAL B  90 "
      ideal   model   delta    sigma   weight residual
     112.96  109.25    3.71 1.00e+00 1.00e+00 1.37e+01
  ... (remaining 11221 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 4489
       17.88 -    35.75: 361
       35.75 -    53.63: 52
       53.63 -    71.51: 9
       71.51 -    89.39: 7
  Dihedral angle restraints: 4918
    sinusoidal: 1924
      harmonic: 2994
  Sorted by residual:
  dihedral pdb=" CB  CYS R 657 "
           pdb=" SG  CYS R 657 "
           pdb=" SG  CYS R 733 "
           pdb=" CB  CYS R 733 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -126.14   40.14     1      1.00e+01 1.00e-02 2.26e+01
  dihedral pdb=" CA  GLY B 202 "
           pdb=" C   GLY B 202 "
           pdb=" N   ALA B 203 "
           pdb=" CA  ALA B 203 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.01  -19.99     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" CA  ASN R 736 "
           pdb=" C   ASN R 736 "
           pdb=" N   TRP R 737 "
           pdb=" CA  TRP R 737 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.84   19.16     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 4915 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 1074
       0.072 -    0.145: 196
       0.145 -    0.217: 15
       0.217 -    0.289: 0
       0.289 -    0.362: 1
  Chirality restraints: 1286
  Sorted by residual:
  chirality pdb=" CA  ALA B 203 "
            pdb=" N   ALA B 203 "
            pdb=" C   ALA B 203 "
            pdb=" CB  ALA B 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.12    0.36 2.00e-01 2.50e+01 3.27e+00
  chirality pdb=" CA  PHE R 663 "
            pdb=" N   PHE R 663 "
            pdb=" C   PHE R 663 "
            pdb=" CB  PHE R 663 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.13e-01
  chirality pdb=" CA  TYR B  59 "
            pdb=" N   TYR B  59 "
            pdb=" C   TYR B  59 "
            pdb=" CB  TYR B  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.07e-01
  ... (remaining 1283 not shown)

  Planarity restraints: 1417
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 666 "   -0.013 2.00e-02 2.50e+03   2.59e-02 6.72e+00
        pdb=" C   PHE R 666 "    0.045 2.00e-02 2.50e+03
        pdb=" O   PHE R 666 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   PHE R 667 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 664 "    0.012 2.00e-02 2.50e+03   2.37e-02 5.61e+00
        pdb=" C   THR R 664 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   THR R 664 "    0.015 2.00e-02 2.50e+03
        pdb=" N   HIS R 665 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 678 "    0.011 2.00e-02 2.50e+03   2.21e-02 4.86e+00
        pdb=" C   LEU R 678 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   LEU R 678 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLY R 679 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1414 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1133
        2.75 -     3.29: 7091
        3.29 -     3.82: 11990
        3.82 -     4.36: 13614
        4.36 -     4.90: 25084
  Nonbonded interactions: 58912
  Sorted by model distance:
  nonbonded pdb=" O   ALA R 818 "
            pdb=" CG2 ILE R 822 "
     model   vdw
     2.209 3.460
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.246 2.440
  nonbonded pdb=" O   ASP B 186 "
            pdb=" O   ALA B 203 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   THR B  86 "
            pdb=" OG1 THR B  87 "
     model   vdw
     2.374 2.440
  nonbonded pdb=" NE2 GLN A  59 "
            pdb=" O   SER A 366 "
     model   vdw
     2.380 2.520
  ... (remaining 58907 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:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          3.840
  Check model and map are aligned:         0.130
  Set scattering table:                    0.070
  Process input model:                     23.510
  Find NCS groups from input model:        0.190
  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:12.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
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      :  0.009   0.052   8283  Z= 0.576
  Angle     :  0.838   8.781  11226  Z= 0.483
  Chirality :  0.054   0.362   1286
  Planarity :  0.006   0.050   1417
  Dihedral  : 13.411  89.387   2977
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 1.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.25), residues: 1020
  helix:  0.11 (0.27), residues: 367
  sheet:  0.57 (0.35), residues: 220
  loop : -2.04 (0.27), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.003   TRP A 234 
   HIS   0.007   0.002   HIS B  62 
   PHE   0.023   0.003   PHE B 151 
   TYR   0.025   0.003   TYR N  80 
   ARG   0.027   0.001   ARG N  72 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.897 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 1.2395
  time to fit residues: 242.2990
Evaluate side-chains
  162 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.869 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2393
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    0.5980
   chunk 75 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   chunk 78 optimal weight:    0.5980
   chunk 30 optimal weight:    0.1980
   chunk 47 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
A 392 ASN
B  75 GLN
R 815 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.1224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8283  Z= 0.215
  Angle     :  0.565   7.549  11226  Z= 0.307
  Chirality :  0.043   0.153   1286
  Planarity :  0.004   0.048   1417
  Dihedral  :  4.691  25.985   1114
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  :  9.02 %
    Favored  : 88.50 %
  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: -0.12 (0.26), residues: 1020
  helix:  1.19 (0.27), residues: 370
  sheet:  0.63 (0.34), residues: 228
  loop : -1.69 (0.28), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.022   0.002   TRP B  82 
   HIS   0.004   0.001   HIS A 357 
   PHE   0.016   0.002   PHE A 212 
   TYR   0.013   0.002   TYR B  59 
   ARG   0.004   0.000   ARG B 134 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 172
  time to evaluate  : 0.839 
Fit side-chains
  outliers start: 22
  outliers final: 9
  residues processed: 183
  average time/residue: 1.2454
  time to fit residues: 240.8482
Evaluate side-chains
  175 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 166
  time to evaluate  : 0.893 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 6
  residues processed: 3
  average time/residue: 0.0711
  time to fit residues: 1.6603
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 81 optimal weight:    0.4980
   chunk 31 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
A 392 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.1348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   8283  Z= 0.270
  Angle     :  0.581   7.302  11226  Z= 0.313
  Chirality :  0.044   0.151   1286
  Planarity :  0.004   0.047   1417
  Dihedral  :  4.645  24.791   1114
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 11.84 %
    Favored  : 85.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.26), residues: 1020
  helix:  1.48 (0.27), residues: 371
  sheet:  0.61 (0.33), residues: 236
  loop : -1.61 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.019   0.002   TRP B  82 
   HIS   0.004   0.001   HIS A 357 
   PHE   0.016   0.002   PHE A 212 
   TYR   0.015   0.002   TYR N  95 
   ARG   0.005   0.000   ARG B 219 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 166
  time to evaluate  : 0.820 
Fit side-chains
  outliers start: 28
  outliers final: 17
  residues processed: 180
  average time/residue: 1.2989
  time to fit residues: 247.7984
Evaluate side-chains
  179 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 162
  time to evaluate  : 0.929 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 8
  residues processed: 9
  average time/residue: 0.4276
  time to fit residues: 5.7801
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0870
   chunk 61 optimal weight:    2.9990
   chunk 91 optimal weight:    0.5980
   chunk 96 optimal weight:    1.9990
   chunk 86 optimal weight:    0.3980
   chunk 26 optimal weight:    0.0060
   chunk 80 optimal weight:    0.5980
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.3374

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
B 155 ASN
N  84 ASN
R 696 HIS
R 830 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.1837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8283  Z= 0.146
  Angle     :  0.505   7.570  11226  Z= 0.271
  Chirality :  0.042   0.140   1286
  Planarity :  0.003   0.044   1417
  Dihedral  :  4.256  24.257   1114
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 13.42 %
    Favored  : 84.22 %
  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:  0.39 (0.27), residues: 1020
  helix:  1.91 (0.28), residues: 370
  sheet:  0.69 (0.33), residues: 233
  loop : -1.59 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.001   TRP B  82 
   HIS   0.004   0.001   HIS R 696 
   PHE   0.013   0.001   PHE A 212 
   TYR   0.011   0.001   TYR B 124 
   ARG   0.006   0.000   ARG B 219 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 169
  time to evaluate  : 0.921 
Fit side-chains
  outliers start: 21
  outliers final: 9
  residues processed: 184
  average time/residue: 1.2533
  time to fit residues: 244.2647
Evaluate side-chains
  170 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 161
  time to evaluate  : 0.926 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 9
  residues processed: 0
  time to fit residues: 1.3564
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 71 optimal weight:    0.0980
   chunk 39 optimal weight:    0.8980
   chunk 82 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0570
   chunk 87 optimal weight:    0.1980
   overall best weight:    0.3698

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
A 392 ASN
B 155 ASN
N  31 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7359
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8283  Z= 0.157
  Angle     :  0.503   6.812  11226  Z= 0.271
  Chirality :  0.041   0.139   1286
  Planarity :  0.003   0.042   1417
  Dihedral  :  4.195  24.611   1114
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 15.11 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.27), residues: 1020
  helix:  2.04 (0.28), residues: 371
  sheet:  0.78 (0.33), residues: 238
  loop : -1.50 (0.29), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.001   TRP B  82 
   HIS   0.004   0.001   HIS A 357 
   PHE   0.014   0.001   PHE A 212 
   TYR   0.012   0.001   TYR N  95 
   ARG   0.006   0.000   ARG B 219 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 159
  time to evaluate  : 0.921 
Fit side-chains
  outliers start: 24
  outliers final: 15
  residues processed: 173
  average time/residue: 1.3596
  time to fit residues: 248.5185
Evaluate side-chains
  167 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 152
  time to evaluate  : 0.843 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 9
  residues processed: 6
  average time/residue: 0.7693
  time to fit residues: 6.2985
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 96 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 50 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
A 392 ASN
B 155 ASN
N  31 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   8283  Z= 0.260
  Angle     :  0.568   8.699  11226  Z= 0.303
  Chirality :  0.043   0.141   1286
  Planarity :  0.004   0.042   1417
  Dihedral  :  4.400  24.758   1114
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.69 %
    Favored  : 80.72 %
  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:  0.49 (0.27), residues: 1020
  helix:  1.92 (0.28), residues: 371
  sheet:  0.80 (0.33), residues: 235
  loop : -1.52 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.002   TRP B  82 
   HIS   0.005   0.001   HIS A 357 
   PHE   0.017   0.002   PHE A 212 
   TYR   0.016   0.002   TYR N  95 
   ARG   0.007   0.000   ARG B 219 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 156
  time to evaluate  : 0.923 
Fit side-chains
  outliers start: 23
  outliers final: 15
  residues processed: 170
  average time/residue: 1.2329
  time to fit residues: 222.0680
Evaluate side-chains
  167 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 152
  time to evaluate  : 0.935 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 11
  residues processed: 4
  average time/residue: 0.3687
  time to fit residues: 3.0315
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 54 optimal weight:    0.3980
   chunk 81 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0370
   chunk 58 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0980
   chunk 38 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.3858

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
B 155 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8283  Z= 0.162
  Angle     :  0.504   6.021  11226  Z= 0.271
  Chirality :  0.041   0.152   1286
  Planarity :  0.003   0.041   1417
  Dihedral  :  4.188  24.038   1114
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 17.93 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.27), residues: 1020
  helix:  2.10 (0.28), residues: 371
  sheet:  0.84 (0.33), residues: 239
  loop : -1.48 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.019   0.001   TRP B  82 
   HIS   0.003   0.001   HIS A 357 
   PHE   0.014   0.001   PHE A 212 
   TYR   0.013   0.001   TYR N  95 
   ARG   0.006   0.000   ARG B 219 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 155
  time to evaluate  : 0.994 
Fit side-chains
  outliers start: 20
  outliers final: 16
  residues processed: 168
  average time/residue: 1.2520
  time to fit residues: 222.6587
Evaluate side-chains
  169 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 153
  time to evaluate  : 0.821 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 12
  residues processed: 4
  average time/residue: 0.6069
  time to fit residues: 3.8023
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 8 optimal weight:    0.4980
   chunk 75 optimal weight:    3.9990
   chunk 87 optimal weight:    0.0570
   chunk 92 optimal weight:    0.9990
   chunk 84 optimal weight:    0.8980
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
A 392 ASN
B 155 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.2013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8283  Z= 0.199
  Angle     :  0.527   6.477  11226  Z= 0.283
  Chirality :  0.042   0.155   1286
  Planarity :  0.003   0.041   1417
  Dihedral  :  4.227  24.759   1114
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 18.26 %
    Favored  : 79.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.63 (0.27), residues: 1020
  helix:  2.09 (0.28), residues: 371
  sheet:  0.74 (0.33), residues: 242
  loop : -1.44 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.001   TRP B  82 
   HIS   0.004   0.001   HIS A 357 
   PHE   0.015   0.001   PHE A 212 
   TYR   0.014   0.001   TYR N  95 
   ARG   0.007   0.000   ARG B 219 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 152
  time to evaluate  : 0.924 
Fit side-chains
  outliers start: 19
  outliers final: 14
  residues processed: 167
  average time/residue: 1.3538
  time to fit residues: 239.1515
Evaluate side-chains
  162 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 148
  time to evaluate  : 1.230 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 12
  residues processed: 3
  average time/residue: 0.1504
  time to fit residues: 2.0516
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    0.5980
   chunk 54 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 70 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 81 optimal weight:    0.6980
   chunk 84 optimal weight:    0.6980
   chunk 89 optimal weight:    0.0970
   chunk 58 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
A 392 ASN
B 155 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.2012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8283  Z= 0.211
  Angle     :  0.535   6.696  11226  Z= 0.288
  Chirality :  0.042   0.153   1286
  Planarity :  0.004   0.041   1417
  Dihedral  :  4.267  25.234   1114
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 18.15 %
    Favored  : 79.48 %
  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:  0.62 (0.27), residues: 1020
  helix:  2.09 (0.28), residues: 372
  sheet:  0.71 (0.33), residues: 242
  loop : -1.44 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.001   TRP B  82 
   HIS   0.005   0.001   HIS A 357 
   PHE   0.016   0.002   PHE A 212 
   TYR   0.015   0.001   TYR N  95 
   ARG   0.007   0.000   ARG B 219 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 152
  time to evaluate  : 0.886 
Fit side-chains
  outliers start: 21
  outliers final: 15
  residues processed: 168
  average time/residue: 1.3289
  time to fit residues: 236.4144
Evaluate side-chains
  166 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 151
  time to evaluate  : 0.895 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 13
  residues processed: 3
  average time/residue: 0.1542
  time to fit residues: 1.9443
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 99 optimal weight:    0.5980
   chunk 91 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9990
   chunk 84 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
B 155 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.1967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   8283  Z= 0.251
  Angle     :  0.561   8.432  11226  Z= 0.301
  Chirality :  0.043   0.151   1286
  Planarity :  0.004   0.041   1417
  Dihedral  :  4.373  26.061   1114
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 18.94 %
    Favored  : 79.03 %
  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:  0.59 (0.27), residues: 1020
  helix:  2.04 (0.28), residues: 372
  sheet:  0.68 (0.33), residues: 241
  loop : -1.42 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.002   TRP B  82 
   HIS   0.006   0.001   HIS A 357 
   PHE   0.016   0.002   PHE A 212 
   TYR   0.016   0.002   TYR N  95 
   ARG   0.007   0.000   ARG B 219 

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 150
  time to evaluate  : 0.944 
Fit side-chains
  outliers start: 18
  outliers final: 15
  residues processed: 163
  average time/residue: 1.3107
  time to fit residues: 225.9706
Evaluate side-chains
  164 residues out of total 887 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 149
  time to evaluate  : 0.868 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 14
  residues processed: 2
  average time/residue: 0.1268
  time to fit residues: 1.6218
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 79 optimal weight:    0.2980
   chunk 33 optimal weight:    0.9980
   chunk 81 optimal weight:    0.0070
   chunk 10 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
B  75 GLN
B 155 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.134013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.112759 restraints weight = 11567.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 2.27
r_work: 0.3332 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8283  Z= 0.200
  Angle     :  0.535   7.368  11226  Z= 0.287
  Chirality :  0.042   0.153   1286
  Planarity :  0.003   0.041   1417
  Dihedral  :  4.267  25.705   1114
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 19.05 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.27), residues: 1020
  helix:  2.12 (0.28), residues: 372
  sheet:  0.70 (0.33), residues: 242
  loop : -1.43 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.019   0.001   TRP B  82 
   HIS   0.005   0.001   HIS A 357 
   PHE   0.015   0.001   PHE A 212 
   TYR   0.014   0.001   TYR N  95 
   ARG   0.007   0.000   ARG B 219 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4061.60 seconds
wall clock time: 72 minutes 13.43 seconds (4333.43 seconds total)