Starting phenix.real_space_refine
on Fri Dec  8 10:30:26 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxw_32882/12_2023/7wxw_32882_neut.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxw_32882/12_2023/7wxw_32882.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxw_32882/12_2023/7wxw_32882.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxw_32882/12_2023/7wxw_32882.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxw_32882/12_2023/7wxw_32882_neut.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxw_32882/12_2023/7wxw_32882_neut.pdb"
  }
  resolution = 2.84
  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=   0.020
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    5176      2.51       5
     N    1407      2.21       5
     O    1486      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "R PHE  569": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R TYR  590": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE  667": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE  672": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R TYR  727": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE  759": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R PHE  833": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   61": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU   21": "OE1" <-> "OE2"
    Residue "A PHE  208": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  212": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  219": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  222": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  238": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  253": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  311": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  312": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  330": "OE1" <-> "OE2"
    Residue "A TYR  339": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  345": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  358": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  360": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  363": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  381": "OD1" <-> "OD2"
    Residue "D PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE   29": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE  103": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP  106": "OD1" <-> "OD2"
    Residue "B ASP   76": "OD1" <-> "OD2"
    Residue "B TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  180": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  199": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  222": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  234": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  241": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  253": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  264": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  335": "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: 8121
  Number of models: 1
  Model: ""
    Number of chains: 5
    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
    Chain: "C"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 433
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "A"
      Number of atoms: 1942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1942
          Classifications: {'peptide': 234}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 331}
  Time building chain proxies: 4.78, per 1000 atoms: 0.59
  Number of scatterers: 8121
  At special positions: 0
  Unit cell: (84.7, 100.1, 133.1, 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    1486      8.00
     N    1407      7.00
     C    5176      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 657 " - pdb=" SG  CYS R 733 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.91
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1934

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 10 sheets defined
      40.8% alpha, 19.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'R' and resid 568 through 573
      removed outlier: 3.978A  pdb=" N   LEU R 572 " --> pdb=" O   PHE R 569 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 581 through 610
      removed outlier: 3.700A  pdb=" N   LYS R 586 " --> pdb=" O   PHE R 582 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   TRP R 587 " --> pdb=" O   PRO R 583 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   ILE R 588 " --> pdb=" O   VAL R 584 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   GLY R 594 " --> pdb=" O   TYR R 590 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   PHE R 610 " --> pdb=" O   ILE R 606 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 617 through 646
      removed outlier: 3.712A  pdb=" N   THR R 646 " --> pdb=" O   ILE R 642 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 655 through 687
      removed outlier: 3.892A  pdb=" N   ALA R 659 " --> pdb=" O   GLY R 655 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   VAL R 661 " --> pdb=" O   CYS R 657 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 694 through 707
      removed outlier: 3.573A  pdb=" N   MET R 698 " --> pdb=" O   ALA R 694 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 708 through 722
      removed outlier: 3.556A  pdb=" N   ILE R 712 " --> pdb=" O   GLY R 708 " (cutoff:3.500A)
    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 767
      Proline residue:  R 750  - end of helix
      removed outlier: 3.607A  pdb=" N   ALA R 753 " --> pdb=" O   VAL R 749 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   ILE R 754 " --> pdb=" O   PRO R 750 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL R 755 " --> pdb=" O   ALA R 751 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   VAL R 757 " --> pdb=" O   ALA R 753 " (cutoff:3.500A)
      removed outlier: 4.938A  pdb=" N   VAL R 760 " --> pdb=" O   ALA R 756 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 785 through 794
    Processing helix  chain 'R' and resid 795 through 801
      removed outlier: 4.153A  pdb=" N   LEU R 799 " --> pdb=" O   ILE R 795 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU R 800 " --> pdb=" O   LEU R 796 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 802 through 805
    Processing helix  chain 'R' and resid 806 through 811
      removed outlier: 3.969A  pdb=" N   THR R 810 " --> pdb=" O   PHE R 806 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE R 811 " --> pdb=" O   GLY R 807 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 806 through 811'
    Processing helix  chain 'R' and resid 818 through 828
      removed outlier: 3.654A  pdb=" N   PHE R 823 " --> pdb=" O   TRP R 819 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   ALA R 824 " --> pdb=" O   HIS R 820 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 829 through 838
    Processing helix  chain 'R' and resid 842 through 854
      removed outlier: 3.623A  pdb=" N   ARG R 846 " --> pdb=" O   ASP R 842 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 9 through 23
    Processing helix  chain 'C' and resid 31 through 44
      removed outlier: 4.029A  pdb=" N   ALA C  35 " --> pdb=" O   SER C  31 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ASP C  36 " --> pdb=" O   LYS C  32 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   LEU C  37 " --> pdb=" O   ALA C  33 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   CYS C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLU C  42 " --> pdb=" O   MET C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 55 through 59
      removed outlier: 3.538A  pdb=" N   ASN C  59 " --> pdb=" O   ALA C  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 13 through 39
      removed outlier: 3.629A  pdb=" N   GLN A  29 " --> pdb=" O   MET A  25 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 61
      removed outlier: 3.780A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   VAL A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 64
      No H-bonds generated for 'chain 'A' and resid 62 through 64'
    Processing helix  chain 'A' and resid 234 through 239
      removed outlier: 3.676A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
      removed outlier: 3.547A  pdb=" N   SER A 275 " --> pdb=" O   ASN A 271 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ILE A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.993A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ALA A 298 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 318
      removed outlier: 3.677A  pdb=" N   TYR A 318 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.710A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ARG A 342 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 390
      removed outlier: 3.640A  pdb=" N   ARG A 374 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ILE A 375 " --> pdb=" O   ASN A 371 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 28 through 32
      removed outlier: 3.669A  pdb=" N   ASN D  31 " --> pdb=" O   THR D  28 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   TYR D  32 " --> pdb=" O   PHE D  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 28 through 32'
    Processing helix  chain 'D' and resid 62 through 65
      removed outlier: 3.734A  pdb=" N   LYS D  65 " --> pdb=" O   GLY D  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 62 through 65'
    Processing helix  chain 'D' and resid 87 through 91
      removed outlier: 3.551A  pdb=" N   THR D  91 " --> pdb=" O   PRO D  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 24
      removed outlier: 3.684A  pdb=" N   ALA B  24 " --> pdb=" O   ASP B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214
      removed outlier: 6.379A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 10.330A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.383A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.920A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.530A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 7
      removed outlier: 3.646A  pdb=" N   LEU D  18 " --> pdb=" O   MET D  83 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   MET D  83 " --> pdb=" O   LEU D  18 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   SER D  71 " --> pdb=" O   TYR D  80 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.125A  pdb=" N   GLY D  10 " --> pdb=" O   THR D 125 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   VAL D  93 " --> pdb=" O   GLN D  39 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   MET D  34 " --> pdb=" O   ILE D  51 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ILE D  51 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   SER D  49 " --> pdb=" O   TRP D  36 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   SER D  59 " --> pdb=" O   ASP D  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.917A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY B 330 " --> pdb=" O   CYS B 317 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.147A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.262A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.907A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.698A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.975A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.283A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151
      removed outlier: 7.074A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.261A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.891A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.992A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.943A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.126A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    330 hydrogen bonds defined for protein.
    924 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: 2.53

  Time building geometry restraints manager: 3.20 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: 2636
        1.34 -     1.46: 2015
        1.46 -     1.59: 3567
        1.59 -     1.71: 0
        1.71 -     1.83: 74
  Bond restraints: 8292
  Sorted by residual:
  bond pdb=" CA  GLY R 655 "
       pdb=" C   GLY R 655 "
    ideal  model  delta    sigma   weight residual
    1.514  1.531 -0.016 1.41e-02 5.03e+03 1.34e+00
  bond pdb=" CA  GLY B  64 "
       pdb=" C   GLY B  64 "
    ideal  model  delta    sigma   weight residual
    1.522  1.510  0.012 1.06e-02 8.90e+03 1.28e+00
  bond pdb=" CG  LEU D  20 "
       pdb=" CD1 LEU D  20 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.26e+00
  bond pdb=" CA  HIS R 665 "
       pdb=" C   HIS R 665 "
    ideal  model  delta    sigma   weight residual
    1.524  1.510  0.014 1.28e-02 6.10e+03 1.23e+00
  bond pdb=" N   GLY R 655 "
       pdb=" CA  GLY R 655 "
    ideal  model  delta    sigma   weight residual
    1.449  1.465 -0.016 1.45e-02 4.76e+03 1.19e+00
  ... (remaining 8287 not shown)

  Histogram of bond angle deviations from ideal:
       99.18 -   106.16: 159
      106.16 -   113.14: 4468
      113.14 -   120.12: 3038
      120.12 -   127.10: 3482
      127.10 -   134.08: 91
  Bond angle restraints: 11238
  Sorted by residual:
  angle pdb=" C   ASP B 291 "
        pdb=" N   PHE B 292 "
        pdb=" CA  PHE B 292 "
      ideal   model   delta    sigma   weight residual
     121.70  128.85   -7.15 1.80e+00 3.09e-01 1.58e+01
  angle pdb=" N   ASP B 291 "
        pdb=" CA  ASP B 291 "
        pdb=" C   ASP B 291 "
      ideal   model   delta    sigma   weight residual
     110.80  118.53   -7.73 2.13e+00 2.20e-01 1.32e+01
  angle pdb=" N   ALA B 104 "
        pdb=" CA  ALA B 104 "
        pdb=" C   ALA B 104 "
      ideal   model   delta    sigma   weight residual
     108.46  113.90   -5.44 1.51e+00 4.39e-01 1.30e+01
  angle pdb=" N   TYR D  94 "
        pdb=" CA  TYR D  94 "
        pdb=" C   TYR D  94 "
      ideal   model   delta    sigma   weight residual
     108.41  113.97   -5.56 1.63e+00 3.76e-01 1.16e+01
  angle pdb=" N   LYS A  17 "
        pdb=" CA  LYS A  17 "
        pdb=" C   LYS A  17 "
      ideal   model   delta    sigma   weight residual
     111.07  107.44    3.63 1.07e+00 8.73e-01 1.15e+01
  ... (remaining 11233 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.16: 4559
       18.16 -    36.32: 298
       36.32 -    54.48: 44
       54.48 -    72.64: 11
       72.64 -    90.79: 7
  Dihedral angle restraints: 4919
    sinusoidal: 1930
      harmonic: 2989
  Sorted by residual:
  dihedral pdb=" CA  GLN R 815 "
           pdb=" C   GLN R 815 "
           pdb=" N   ASN R 816 "
           pdb=" CA  ASN R 816 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.00  -42.00     0      5.00e+00 4.00e-02 7.06e+01
  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 -130.02   44.02     1      1.00e+01 1.00e-02 2.70e+01
  dihedral pdb=" CA  ALA B 104 "
           pdb=" C   ALA B 104 "
           pdb=" N   TYR B 105 "
           pdb=" CA  TYR B 105 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.17   19.83     0      5.00e+00 4.00e-02 1.57e+01
  ... (remaining 4916 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1095
       0.069 -    0.137: 171
       0.137 -    0.206: 10
       0.206 -    0.275: 3
       0.275 -    0.343: 1
  Chirality restraints: 1280
  Sorted by residual:
  chirality pdb=" CA  CYS R 657 "
            pdb=" N   CYS R 657 "
            pdb=" C   CYS R 657 "
            pdb=" CB  CYS R 657 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.95e+00
  chirality pdb=" CA  GLN B  75 "
            pdb=" N   GLN B  75 "
            pdb=" C   GLN B  75 "
            pdb=" CB  GLN B  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CA  THR B 196 "
            pdb=" N   THR B 196 "
            pdb=" C   THR B 196 "
            pdb=" CB  THR B 196 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.29    0.23 2.00e-01 2.50e+01 1.36e+00
  ... (remaining 1277 not shown)

  Planarity restraints: 1421
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 666 "    0.013 2.00e-02 2.50e+03   2.66e-02 7.08e+00
        pdb=" C   PHE R 666 "   -0.046 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=" C   PHE B 235 "    0.043 5.00e-02 4.00e+02   6.55e-02 6.86e+00
        pdb=" N   PRO B 236 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R 664 "   -0.012 2.00e-02 2.50e+03   2.50e-02 6.27e+00
        pdb=" C   THR R 664 "    0.043 2.00e-02 2.50e+03
        pdb=" O   THR R 664 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   HIS R 665 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1418 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.78: 1854
        2.78 -     3.31: 6917
        3.31 -     3.84: 12032
        3.84 -     4.37: 13717
        4.37 -     4.90: 25112
  Nonbonded interactions: 59632
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.256 2.440
  nonbonded pdb=" OD1 ASP R 813 "
            pdb=" N   SER R 814 "
     model   vdw
     2.264 2.520
  nonbonded pdb=" O   ARG B 314 "
            pdb=" OG  SER B 331 "
     model   vdw
     2.315 2.440
  nonbonded pdb=" OD1 ASP D  50 "
            pdb=" N   ILE D  51 "
     model   vdw
     2.333 2.520
  nonbonded pdb=" OD1 ASP B 163 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.334 2.440
  ... (remaining 59627 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:             1.280
  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:          3.860
  Check model and map are aligned:         0.110
  Set scattering table:                    0.070
  Process input model:                     24.720
  Find NCS groups from input model:        0.240
  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:13.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
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   0.044   8292  Z= 0.329
  Angle     :  0.779   8.363  11238  Z= 0.454
  Chirality :  0.050   0.343   1280
  Planarity :  0.006   0.066   1421
  Dihedral  : 12.888  90.794   2979
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 1.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.04 (0.23), residues: 1018
  helix: -0.95 (0.26), residues: 356
  sheet: -0.03 (0.36), residues: 197
  loop : -2.27 (0.23), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.029   0.003   TRP B  82 
   HIS   0.009   0.002   HIS A 357 
   PHE   0.021   0.002   PHE R 569 
   TYR   0.021   0.002   TYR D  95 
   ARG   0.005   0.000   ARG B 150 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 885 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 1.1382
  time to fit residues: 231.6548
Evaluate side-chains
  171 residues out of total 885 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.913 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3032
-------------------------------------------------------------------------------
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:    0.9990
   chunk 75 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0770
   chunk 47 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   chunk 90 optimal weight:    0.0370
   overall best weight:    0.5616

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

Flipped N/Q/H residues before XYZ refinement:
R 695 GLN
R 815 GLN
A  29 GLN
A 236 GLN
B  88 ASN
B 176 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.1166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8292  Z= 0.214
  Angle     :  0.571   7.943  11238  Z= 0.307
  Chirality :  0.043   0.139   1280
  Planarity :  0.005   0.059   1421
  Dihedral  :  5.051  42.706   1115
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 10.73 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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 (0.25), residues: 1018
  helix:  0.30 (0.27), residues: 353
  sheet:  0.35 (0.36), residues: 199
  loop : -2.00 (0.24), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.002   TRP B  82 
   HIS   0.006   0.001   HIS A 357 
   PHE   0.019   0.002   PHE R 667 
   TYR   0.016   0.001   TYR D  95 
   ARG   0.004   0.000   ARG D 118 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 885 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 176
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
  outliers start: 18
  outliers final: 9
  residues processed: 179
  average time/residue: 1.2267
  time to fit residues: 232.3563
Evaluate side-chains
  174 residues out of total 885 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 165
  time to evaluate  : 0.892 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 3
  residues processed: 6
  average time/residue: 0.9911
  time to fit residues: 7.5963
-------------------------------------------------------------------------------
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:    0.9990
   chunk 28 optimal weight:    7.9990
   chunk 75 optimal weight:    0.0270
   chunk 61 optimal weight:    0.0770
   chunk 25 optimal weight:    2.9990
   chunk 90 optimal weight:    0.5980
   chunk 98 optimal weight:    2.9990
   chunk 81 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9990
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
R 815 GLN
C  59 ASN
A 236 GLN
B 176 GLN
B 340 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8292  Z= 0.184
  Angle     :  0.529   8.444  11238  Z= 0.283
  Chirality :  0.042   0.135   1280
  Planarity :  0.004   0.060   1421
  Dihedral  :  4.637  38.342   1115
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 12.20 %
    Favored  : 85.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.53 (0.25), residues: 1018
  helix:  0.98 (0.28), residues: 350
  sheet:  0.52 (0.37), residues: 198
  loop : -1.84 (0.25), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.002   TRP B  82 
   HIS   0.005   0.001   HIS A 357 
   PHE   0.019   0.001   PHE R 667 
   TYR   0.018   0.001   TYR D  60 
   ARG   0.003   0.000   ARG D 118 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 885 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 166
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
  outliers start: 24
  outliers final: 9
  residues processed: 173
  average time/residue: 1.2527
  time to fit residues: 229.2281
Evaluate side-chains
  171 residues out of total 885 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 162
  time to evaluate  : 0.875 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 4
  residues processed: 5
  average time/residue: 0.2972
  time to fit residues: 3.0467
-------------------------------------------------------------------------------
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:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9980
   chunk 86 optimal weight:    0.8980
   chunk 26 optimal weight:    6.9990
   chunk 80 optimal weight:    0.0970
   chunk 54 optimal weight:    0.5980
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
R 815 GLN
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 GLN
D  31 ASN
B 176 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7110
moved from start:          0.1761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8292  Z= 0.253
  Angle     :  0.581   9.600  11238  Z= 0.306
  Chirality :  0.043   0.145   1280
  Planarity :  0.004   0.058   1421
  Dihedral  :  4.719  37.871   1115
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 13.67 %
    Favored  : 82.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.37 (0.26), residues: 1018
  helix:  1.07 (0.28), residues: 350
  sheet:  0.69 (0.35), residues: 219
  loop : -1.86 (0.25), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.021   0.002   TRP B  82 
   HIS   0.007   0.001   HIS A 357 
   PHE   0.020   0.002   PHE R 667 
   TYR   0.019   0.002   TYR D  60 
   ARG   0.003   0.000   ARG D 118 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 885 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 159
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
  outliers start: 31
  outliers final: 20
  residues processed: 172
  average time/residue: 1.3222
  time to fit residues: 240.2894
Evaluate side-chains
  175 residues out of total 885 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 155
  time to evaluate  : 0.918 
Switching outliers to nearest non-outliers
  outliers start: 20
  outliers final: 10
  residues processed: 10
  average time/residue: 0.3709
  time to fit residues: 5.7199
-------------------------------------------------------------------------------
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:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 39 optimal weight:    0.3980
   chunk 82 optimal weight:    0.0050
   chunk 66 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
R 815 GLN
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 GLN
D  31 ASN
B 176 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7090
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8292  Z= 0.202
  Angle     :  0.541   9.621  11238  Z= 0.284
  Chirality :  0.042   0.137   1280
  Planarity :  0.004   0.057   1421
  Dihedral  :  4.483  33.559   1115
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 15.25 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.26), residues: 1018
  helix:  1.31 (0.28), residues: 350
  sheet:  0.64 (0.36), residues: 214
  loop : -1.72 (0.26), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.001   TRP B  82 
   HIS   0.006   0.001   HIS A 357 
   PHE   0.018   0.002   PHE R 667 
   TYR   0.020   0.001   TYR D  60 
   ARG   0.003   0.000   ARG B  52 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 885 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 156
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
  outliers start: 24
  outliers final: 13
  residues processed: 169
  average time/residue: 1.2844
  time to fit residues: 229.1866
Evaluate side-chains
  169 residues out of total 885 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 156
  time to evaluate  : 0.838 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 10
  residues processed: 3
  average time/residue: 0.1497
  time to fit residues: 1.8439
-------------------------------------------------------------------------------
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:    0.4980
   chunk 56 optimal weight:    0.0970
   chunk 23 optimal weight:    0.4980
   chunk 96 optimal weight:    2.9990
   chunk 80 optimal weight:    0.0060
   chunk 44 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 50 optimal weight:    0.4980
   chunk 93 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.3194

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

Flipped N/Q/H residues before XYZ refinement:
R 815 GLN
A 236 GLN
D  31 ASN
B 176 GLN
B 220 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7063
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8292  Z= 0.152
  Angle     :  0.509   9.240  11238  Z= 0.267
  Chirality :  0.041   0.132   1280
  Planarity :  0.004   0.055   1421
  Dihedral  :  4.198  27.463   1115
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 16.38 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.26), residues: 1018
  helix:  1.53 (0.29), residues: 350
  sheet:  0.71 (0.36), residues: 213
  loop : -1.57 (0.26), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP B  82 
   HIS   0.004   0.001   HIS A 357 
   PHE   0.016   0.001   PHE R 667 
   TYR   0.021   0.001   TYR D  60 
   ARG   0.003   0.000   ARG B  52 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 885 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 159
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
  outliers start: 22
  outliers final: 16
  residues processed: 173
  average time/residue: 1.3686
  time to fit residues: 249.5960
Evaluate side-chains
  173 residues out of total 885 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 157
  time to evaluate  : 0.885 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 12
  residues processed: 4
  average time/residue: 0.4250
  time to fit residues: 3.2677
-------------------------------------------------------------------------------
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:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 54 optimal weight:    0.7980
   chunk 81 optimal weight:    0.0970
   chunk 96 optimal weight:    0.6980
   chunk 60 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
R 815 GLN
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 GLN
A 294 GLN
D  31 ASN
B 176 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7090
moved from start:          0.2149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8292  Z= 0.209
  Angle     :  0.544   9.740  11238  Z= 0.285
  Chirality :  0.042   0.140   1280
  Planarity :  0.004   0.055   1421
  Dihedral  :  4.307  23.934   1115
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 16.84 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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:  0.07 (0.26), residues: 1018
  helix:  1.53 (0.29), residues: 350
  sheet:  0.80 (0.35), residues: 224
  loop : -1.64 (0.26), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.001   TRP B  82 
   HIS   0.006   0.001   HIS A 357 
   PHE   0.018   0.002   PHE R 667 
   TYR   0.019   0.001   TYR D  60 
   ARG   0.002   0.000   ARG A  22 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 885 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 160
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
  outliers start: 21
  outliers final: 16
  residues processed: 175
  average time/residue: 1.3319
  time to fit residues: 245.8653
Evaluate side-chains
  174 residues out of total 885 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 158
  time to evaluate  : 0.806 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 12
  residues processed: 4
  average time/residue: 0.1554
  time to fit residues: 2.0095
-------------------------------------------------------------------------------
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:    0.1980
   chunk 18 optimal weight:    0.0170
   chunk 61 optimal weight:    0.5980
   chunk 65 optimal weight:    0.0470
   chunk 47 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0270
   chunk 75 optimal weight:    0.1980
   chunk 87 optimal weight:    0.9990
   chunk 92 optimal weight:    0.8980
   chunk 84 optimal weight:    0.5980
   chunk 89 optimal weight:    0.5980
   overall best weight:    0.0974

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

Flipped N/Q/H residues before XYZ refinement:
R 665 HIS
A 236 GLN
A 294 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7002
moved from start:          0.2654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8292  Z= 0.121
  Angle     :  0.482   8.901  11238  Z= 0.250
  Chirality :  0.040   0.129   1280
  Planarity :  0.003   0.052   1421
  Dihedral  :  3.804  18.532   1115
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 17.85 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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:  0.33 (0.27), residues: 1018
  helix:  1.81 (0.29), residues: 353
  sheet:  0.76 (0.36), residues: 217
  loop : -1.44 (0.26), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP R 734 
   HIS   0.002   0.000   HIS R 696 
   PHE   0.011   0.001   PHE R 667 
   TYR   0.022   0.001   TYR D  60 
   ARG   0.004   0.000   ARG A 356 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 885 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 164
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
  outliers start: 21
  outliers final: 12
  residues processed: 175
  average time/residue: 1.3826
  time to fit residues: 256.7431
Evaluate side-chains
  171 residues out of total 885 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 159
  time to evaluate  : 0.894 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 9
  residues processed: 4
  average time/residue: 0.1564
  time to fit residues: 2.1883
-------------------------------------------------------------------------------
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:    0.6980
   chunk 54 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 27 optimal weight:   20.0000
   chunk 81 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0060
   chunk 89 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 GLN
D  31 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7087
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8292  Z= 0.227
  Angle     :  0.547   6.474  11238  Z= 0.289
  Chirality :  0.042   0.144   1280
  Planarity :  0.004   0.058   1421
  Dihedral  :  4.166  19.692   1115
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 19.55 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.26), residues: 1018
  helix:  1.73 (0.29), residues: 351
  sheet:  0.92 (0.35), residues: 223
  loop : -1.51 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.019   0.002   TRP B  82 
   HIS   0.006   0.001   HIS A 357 
   PHE   0.018   0.002   PHE R 667 
   TYR   0.016   0.001   TYR D  95 
   ARG   0.013   0.000   ARG A 283 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 885 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 158
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
  outliers start: 16
  outliers final: 10
  residues processed: 169
  average time/residue: 1.3944
  time to fit residues: 248.8848
Evaluate side-chains
  168 residues out of total 885 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 158
  time to evaluate  : 0.997 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 9
  residues processed: 1
  average time/residue: 0.2384
  time to fit residues: 1.5719
-------------------------------------------------------------------------------
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:    0.0670
   chunk 66 optimal weight:    0.4980
   chunk 99 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 79 optimal weight:    0.3980
   chunk 8 optimal weight:    0.2980
   chunk 61 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 63 optimal weight:    0.2980
   chunk 84 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0370
   overall best weight:    0.2196

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
A 294 GLN
D  31 ASN
B 176 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8292  Z= 0.139
  Angle     :  0.495   6.114  11238  Z= 0.260
  Chirality :  0.040   0.132   1280
  Planarity :  0.004   0.056   1421
  Dihedral  :  3.872  16.743   1115
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 20.00 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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 (0.27), residues: 1018
  helix:  1.87 (0.29), residues: 353
  sheet:  0.75 (0.36), residues: 220
  loop : -1.38 (0.27), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP B  82 
   HIS   0.003   0.000   HIS A 357 
   PHE   0.014   0.001   PHE R 667 
   TYR   0.018   0.001   TYR D  60 
   ARG   0.012   0.000   ARG A 283 

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

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

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2036 Ramachandran restraints generated.
    1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 885 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 156
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
  outliers start: 15
  outliers final: 12
  residues processed: 168
  average time/residue: 1.3921
  time to fit residues: 246.7234
Evaluate side-chains
  168 residues out of total 885 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 156
  time to evaluate  : 0.834 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 11
  residues processed: 1
  average time/residue: 0.2531
  time to fit residues: 1.5334
-------------------------------------------------------------------------------
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:    0.1980
   chunk 11 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 81 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 14 optimal weight:    0.7980
   chunk 69 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 GLN
D  31 ASN
B 176 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.154249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.128807 restraints weight = 10773.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 2.29
r_work: 0.3550 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3381 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8292  Z= 0.226
  Angle     :  0.545   6.473  11238  Z= 0.288
  Chirality :  0.042   0.143   1280
  Planarity :  0.004   0.055   1421
  Dihedral  :  4.141  18.912   1115
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 19.66 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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:  0.32 (0.26), residues: 1018
  helix:  1.77 (0.29), residues: 351
  sheet:  0.80 (0.35), residues: 229
  loop : -1.47 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP B  82 
   HIS   0.006   0.001   HIS A 357 
   PHE   0.020   0.002   PHE D  68 
   TYR   0.016   0.001   TYR D  95 
   ARG   0.013   0.000   ARG A 283 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4149.89 seconds
wall clock time: 73 minutes 46.33 seconds (4426.33 seconds total)