Starting phenix.real_space_refine
on Fri Dec 15 09:25:50 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utp_26786/12_2023/7utp_26786.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utp_26786/12_2023/7utp_26786.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utp_26786/12_2023/7utp_26786.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utp_26786/12_2023/7utp_26786.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utp_26786/12_2023/7utp_26786.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utp_26786/12_2023/7utp_26786.pdb"
  }
  resolution = 3.8
  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
-------------------------------------------------------------------------------
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=   0.012 sd=   0.080
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     116      5.16       5
     C   19768      2.51       5
     N    5299      2.21       5
     O    5873      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   51": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  146": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  165": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  233": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  261": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  266": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  324": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  342": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  345": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  353": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  380": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  398": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  405": "OD1" <-> "OD2"
    Residue "A PHE  420": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  444": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  448": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  464": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  471": "OD1" <-> "OD2"
    Residue "A PHE  474": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  535": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  559": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G GLU   50": "OE1" <-> "OE2"
    Residue "G TYR  165": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G GLU  193": "OE1" <-> "OE2"
    Residue "G PHE  266": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE  268": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE  398": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G ASP  405": "OD1" <-> "OD2"
    Residue "G TYR  409": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR  444": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE  474": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE  527": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE  535": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G PHE  559": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G TYR  573": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F GLU   60": "OE1" <-> "OE2"
    Residue "F GLU  135": "OE1" <-> "OE2"
    Residue "F PHE  141": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  165": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  210": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  212": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ASP  237": "OD1" <-> "OD2"
    Residue "F PHE  266": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  268": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  303": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  353": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  398": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  444": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  464": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ASP  477": "OD1" <-> "OD2"
    Residue "F ASP  511": "OD1" <-> "OD2"
    Residue "F PHE  527": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F PHE  559": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  561": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F TYR  584": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE   51": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR   79": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP  125": "OD1" <-> "OD2"
    Residue "D PHE  197": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR  464": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE  527": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE  535": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  141": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  185": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  212": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  243": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  261": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  266": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  268": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  290": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ASP  305": "OD1" <-> "OD2"
    Residue "E ASP  413": "OD1" <-> "OD2"
    Residue "E TYR  451": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E TYR  464": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  499": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ASP  513": "OD1" <-> "OD2"
    Residue "E PHE  527": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I PHE   53": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I PHE  121": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I PHE  146": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR  165": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I PHE  185": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I PHE  197": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR  210": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR  233": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I PHE  243": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR  338": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR  342": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I PHE  353": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR  378": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR  400": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I PHE  420": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR  444": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I PHE  474": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I PHE  499": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I PHE  527": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR  561": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  146": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  165": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  185": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  197": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  243": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  261": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  266": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  267": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  499": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  527": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU   60": "OE1" <-> "OE2"
    Residue "B PHE  121": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  144": "OE1" <-> "OE2"
    Residue "B TYR  165": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  197": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  210": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  233": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  244": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  268": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  290": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  353": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  398": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  464": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  474": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  526": "OD1" <-> "OD2"
    Residue "B TYR  573": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  574": "OE1" <-> "OE2"
  Time to flip residues: 0.07s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 31056
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 4238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 532, 4238
          Classifications: {'peptide': 532}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 492}
          Chain breaks: 2
    Chain: "L"
      Number of atoms: 495
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 495
          Classifications: {'peptide': 99}
          Incomplete info: {'truncation_to_alanine': 99}
          Link IDs: {'TRANS': 98}
          Unresolved non-hydrogen bonds: 198
          Unresolved non-hydrogen angles: 297
          Unresolved non-hydrogen dihedrals: 99
          Planarities with less than four sites: {'UNK:plan-1': 99}
          Unresolved non-hydrogen planarities: 99
    Chain: "H"
      Number of atoms: 540
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 540
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 108}
          Link IDs: {'TRANS': 107}
          Unresolved non-hydrogen bonds: 216
          Unresolved non-hydrogen angles: 324
          Unresolved non-hydrogen dihedrals: 108
          Planarities with less than four sites: {'UNK:plan-1': 108}
          Unresolved non-hydrogen planarities: 108
    Chain: "G"
      Number of atoms: 4238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 532, 4238
          Classifications: {'peptide': 532}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 492}
          Chain breaks: 2
    Chain: "F"
      Number of atoms: 4234
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 531, 4234
          Classifications: {'peptide': 531}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 491}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 2234
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2234
          Classifications: {'peptide': 276}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 259}
          Chain breaks: 8
    Chain: "E"
      Number of atoms: 4238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 532, 4238
          Classifications: {'peptide': 532}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 492}
          Chain breaks: 2
    Chain: "I"
      Number of atoms: 4238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 532, 4238
          Classifications: {'peptide': 532}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 492}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 2394
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2394
          Classifications: {'peptide': 299}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 278}
          Chain breaks: 9
    Chain: "B"
      Number of atoms: 4207
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 528, 4207
          Classifications: {'peptide': 528}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 489}
          Chain breaks: 3
  Time building chain proxies: 12.19, per 1000 atoms: 0.39
  Number of scatterers: 31056
  At special positions: 0
  Unit cell: (191.4, 177.1, 137.5, 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     116     16.00
     O    5873      8.00
     N    5299      7.00
     C   19768      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 490 " - pdb=" SG  CYS A 494 " distance=2.07
    Simple disulfide: pdb=" SG  CYS G 490 " - pdb=" SG  CYS G 494 " distance=2.05
    Simple disulfide: pdb=" SG  CYS F 490 " - pdb=" SG  CYS F 494 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 490 " - pdb=" SG  CYS E 494 " distance=2.07
    Simple disulfide: pdb=" SG  CYS I 490 " - pdb=" SG  CYS I 494 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 490 " - pdb=" SG  CYS C 494 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 490 " - pdb=" SG  CYS B 494 " distance=2.06

  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: 8.04
  Conformation dependent library (CDL) restraints added in 3.5 seconds
  

  7372 Ramachandran restraints generated.
    3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  7424

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 57 sheets defined
      10.7% alpha, 12.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 86 through 91
    Processing helix  chain 'A' and resid 116 through 121
      removed outlier: 3.809A  pdb=" N   TRP A 120 " --> pdb=" O   ALA A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 132
    Processing helix  chain 'A' and resid 187 through 192
      removed outlier: 3.542A  pdb=" N   MET A 190 " --> pdb=" O   PRO A 187 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ARG A 191 " --> pdb=" O   ALA A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 241
      removed outlier: 3.531A  pdb=" N   VAL A 241 " --> pdb=" O   PRO A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 285
      removed outlier: 3.560A  pdb=" N   LEU A 285 " --> pdb=" O   ASN A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 313
      removed outlier: 3.583A  pdb=" N   ARG A 313 " --> pdb=" O   GLN A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 413
      removed outlier: 3.731A  pdb=" N   ASP A 413 " --> pdb=" O   PRO A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 448
      removed outlier: 3.779A  pdb=" N   PHE A 448 " --> pdb=" O   THR A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 562
      removed outlier: 3.663A  pdb=" N   TYR A 561 " --> pdb=" O   GLN A 558 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   VAL A 562 " --> pdb=" O   PHE A 559 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 56 through 61
      removed outlier: 4.185A  pdb=" N   UNK H  60 " --> pdb=" O   UNK H  56 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 86 through 91
    Processing helix  chain 'G' and resid 95 through 99
    Processing helix  chain 'G' and resid 116 through 121
      removed outlier: 3.914A  pdb=" N   TRP G 120 " --> pdb=" O   ALA G 116 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 122 through 132
      removed outlier: 3.610A  pdb=" N   THR G 132 " --> pdb=" O   LEU G 128 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 187 through 191
      removed outlier: 3.528A  pdb=" N   MET G 190 " --> pdb=" O   PRO G 187 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 237 through 241
    Processing helix  chain 'G' and resid 245 through 250
      removed outlier: 3.524A  pdb=" N   SER G 249 " --> pdb=" O   THR G 245 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 309 through 313
      removed outlier: 3.727A  pdb=" N   ARG G 313 " --> pdb=" O   GLN G 310 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 409 through 413
      removed outlier: 3.519A  pdb=" N   ASP G 413 " --> pdb=" O   PRO G 410 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 443 through 448
    Processing helix  chain 'G' and resid 554 through 558
      removed outlier: 3.566A  pdb=" N   GLN G 558 " --> pdb=" O   VAL G 555 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 86 through 91
    Processing helix  chain 'F' and resid 116 through 120
    Processing helix  chain 'F' and resid 122 through 132
      removed outlier: 3.644A  pdb=" N   THR F 132 " --> pdb=" O   LEU F 128 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 237 through 241
      removed outlier: 3.720A  pdb=" N   VAL F 241 " --> pdb=" O   PRO F 238 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 245 through 250
      removed outlier: 3.550A  pdb=" N   SER F 249 " --> pdb=" O   THR F 245 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 309 through 313
      removed outlier: 3.762A  pdb=" N   ARG F 313 " --> pdb=" O   GLN F 310 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 409 through 413
    Processing helix  chain 'F' and resid 443 through 448
      removed outlier: 4.267A  pdb=" N   ILE F 447 " --> pdb=" O   ASN F 443 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 557 through 562
      removed outlier: 3.546A  pdb=" N   ASN F 560 " --> pdb=" O   ASN F 557 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   TYR F 561 " --> pdb=" O   GLN F 558 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   VAL F 562 " --> pdb=" O   PHE F 559 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 557 through 562'
    Processing helix  chain 'D' and resid 55 through 57
      No H-bonds generated for 'chain 'D' and resid 55 through 57'
    Processing helix  chain 'D' and resid 116 through 120
    Processing helix  chain 'D' and resid 122 through 127
    Processing helix  chain 'D' and resid 128 through 133
    Processing helix  chain 'D' and resid 245 through 250
      removed outlier: 3.897A  pdb=" N   VAL D 250 " --> pdb=" O   ILE D 246 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 554 through 558
    Processing helix  chain 'E' and resid 86 through 91
    Processing helix  chain 'E' and resid 95 through 99
      removed outlier: 3.805A  pdb=" N   LEU E  98 " --> pdb=" O   ASN E  95 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 116 through 121
      removed outlier: 4.144A  pdb=" N   TRP E 120 " --> pdb=" O   ALA E 116 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 132
      removed outlier: 3.551A  pdb=" N   LEU E 128 " --> pdb=" O   GLY E 124 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 237 through 241
    Processing helix  chain 'E' and resid 245 through 250
    Processing helix  chain 'E' and resid 381 through 385
      removed outlier: 4.195A  pdb=" N   GLY E 385 " --> pdb=" O   ARG E 382 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 443 through 447
    Processing helix  chain 'E' and resid 558 through 562
      removed outlier: 3.922A  pdb=" N   VAL E 562 " --> pdb=" O   PHE E 559 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 86 through 92
      removed outlier: 4.070A  pdb=" N   VAL I  92 " --> pdb=" O   ASP I  88 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 95 through 99
      removed outlier: 3.637A  pdb=" N   ASP I  99 " --> pdb=" O   MET I  96 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 116 through 120
    Processing helix  chain 'I' and resid 122 through 131
      removed outlier: 3.505A  pdb=" N   LEU I 128 " --> pdb=" O   GLY I 124 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 237 through 241
      removed outlier: 3.634A  pdb=" N   ASP I 240 " --> pdb=" O   ASP I 237 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 245 through 250
    Processing helix  chain 'I' and resid 409 through 413
    Processing helix  chain 'I' and resid 443 through 447
    Processing helix  chain 'I' and resid 557 through 561
      removed outlier: 3.605A  pdb=" N   ASN I 560 " --> pdb=" O   ASN I 557 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   TYR I 561 " --> pdb=" O   GLN I 558 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 557 through 561'
    Processing helix  chain 'C' and resid 86 through 91
    Processing helix  chain 'C' and resid 116 through 121
      removed outlier: 4.167A  pdb=" N   TRP C 120 " --> pdb=" O   ALA C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 237 through 241
      removed outlier: 3.621A  pdb=" N   ASP C 240 " --> pdb=" O   ASP C 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 91
    Processing helix  chain 'B' and resid 95 through 99
    Processing helix  chain 'B' and resid 116 through 120
    Processing helix  chain 'B' and resid 122 through 132
      removed outlier: 3.546A  pdb=" N   VAL B 130 " --> pdb=" O   TRP B 126 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   ASN B 131 " --> pdb=" O   GLN B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 192
      removed outlier: 3.534A  pdb=" N   MET B 190 " --> pdb=" O   PRO B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 313
    Processing helix  chain 'B' and resid 381 through 385
      removed outlier: 3.820A  pdb=" N   GLY B 385 " --> pdb=" O   ARG B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 409 through 413
    Processing helix  chain 'B' and resid 443 through 447
    Processing helix  chain 'B' and resid 557 through 562
      removed outlier: 3.593A  pdb=" N   VAL B 562 " --> pdb=" O   PHE B 559 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 53
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 58 through 72
    current: chain 'A' and resid 164 through 167
    Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 84
    Processing sheet with id=AA3, first strand: chain 'A' and resid 215 through 218
      removed outlier: 3.717A  pdb=" N   GLY A 235 " --> pdb=" O   ASP A 215 " (cutoff:3.500A)
      removed outlier: 7.511A  pdb=" N   THR A 217 " --> pdb=" O   TYR A 233 " (cutoff:3.500A)
      removed outlier: 5.741A  pdb=" N   TYR A 233 " --> pdb=" O   THR A 217 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 276 through 278
      removed outlier: 6.237A  pdb=" N   HIS A 277 " --> pdb=" O   ARG A 581 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 315 through 317
      removed outlier: 3.507A  pdb=" N   GLY A 315 " --> pdb=" O   ALA G 379 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   PHE G 398 " --> pdb=" O   TYR G 378 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 335 through 336
      removed outlier: 6.615A  pdb=" N   GLU A 335 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 354
      removed outlier: 3.625A  pdb=" N   SER A 348 " --> pdb=" O   GLY A 351 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ILE F 415 " --> pdb=" O   LEU F 430 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 396 through 399
    Processing sheet with id=AA9, first strand: chain 'A' and resid 429 through 430
      removed outlier: 3.506A  pdb=" N   SER G 348 " --> pdb=" O   GLY G 351 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 6
      removed outlier: 4.612A  pdb=" N   UNK L  18 " --> pdb=" O   UNK L  74 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   UNK L  74 " --> pdb=" O   UNK L  18 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 33 through 36
    Processing sheet with id=AB3, first strand: chain 'H' and resid 19 through 21
    Processing sheet with id=AB4, first strand: chain 'H' and resid 81 through 82
    Processing sheet with id=AB5, first strand: chain 'G' and resid 50 through 53
  WARNING: can't find start of bonding for strands!
    previous: chain 'G' and resid 58 through 72
    current: chain 'G' and resid 164 through 167
    Processing sheet with id=AB6, first strand: chain 'G' and resid 80 through 84
    Processing sheet with id=AB7, first strand: chain 'G' and resid 215 through 217
      removed outlier: 5.949A  pdb=" N   ASP G 215 " --> pdb=" O   HIS G 234 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   THR G 217 " --> pdb=" O   ILE G 232 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ILE G 232 " --> pdb=" O   THR G 217 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'G' and resid 276 through 278
    Processing sheet with id=AB9, first strand: chain 'G' and resid 315 through 317
    Processing sheet with id=AC1, first strand: chain 'G' and resid 335 through 336
      removed outlier: 6.585A  pdb=" N   GLU G 335 " --> pdb=" O   ALA G 456 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC1
    Processing sheet with id=AC2, first strand: chain 'G' and resid 429 through 430
      removed outlier: 3.729A  pdb=" N   GLY F 351 " --> pdb=" O   SER F 348 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 50 through 53
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 58 through 72
    current: chain 'F' and resid 164 through 167
    Processing sheet with id=AC4, first strand: chain 'F' and resid 80 through 84
      removed outlier: 3.504A  pdb=" N   HIS F 102 " --> pdb=" O   VAL F  84 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'F' and resid 216 through 218
    Processing sheet with id=AC6, first strand: chain 'F' and resid 276 through 278
      removed outlier: 5.781A  pdb=" N   HIS F 277 " --> pdb=" O   ARG F 581 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC6
    Processing sheet with id=AC7, first strand: chain 'F' and resid 335 through 336
      removed outlier: 6.875A  pdb=" N   GLU F 335 " --> pdb=" O   ALA F 456 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC7
    Processing sheet with id=AC8, first strand: chain 'D' and resid 44 through 45
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 44 through 45
    current: chain 'E' and resid 102 through 112
  No H-bonds generated for sheet with id=AC8
    Processing sheet with id=AC9, first strand: chain 'D' and resid 49 through 53
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 59 through 72
    current: chain 'D' and resid 164 through 167
    Processing sheet with id=AD1, first strand: chain 'D' and resid 80 through 82
    Processing sheet with id=AD2, first strand: chain 'D' and resid 379 through 380
    Processing sheet with id=AD3, first strand: chain 'E' and resid 50 through 53
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 58 through 72
    current: chain 'E' and resid 164 through 167
    Processing sheet with id=AD4, first strand: chain 'E' and resid 217 through 218
      removed outlier: 3.640A  pdb=" N   THR E 217 " --> pdb=" O   ILE E 232 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ILE E 232 " --> pdb=" O   THR E 217 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD4
    Processing sheet with id=AD5, first strand: chain 'E' and resid 335 through 336
      removed outlier: 6.637A  pdb=" N   GLU E 335 " --> pdb=" O   ALA E 456 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD5
    Processing sheet with id=AD6, first strand: chain 'E' and resid 345 through 346
    Processing sheet with id=AD7, first strand: chain 'E' and resid 377 through 380
    Processing sheet with id=AD8, first strand: chain 'E' and resid 463 through 464
      removed outlier: 4.354A  pdb=" N   TYR E 464 " --> pdb=" O   GLU E 574 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLU E 574 " --> pdb=" O   TYR E 464 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD8
    Processing sheet with id=AD9, first strand: chain 'I' and resid 49 through 53
  WARNING: can't find start of bonding for strands!
    previous: chain 'I' and resid 58 through 72
    current: chain 'I' and resid 164 through 167
    Processing sheet with id=AE1, first strand: chain 'I' and resid 80 through 84
    Processing sheet with id=AE2, first strand: chain 'I' and resid 216 through 218
      removed outlier: 3.769A  pdb=" N   THR I 217 " --> pdb=" O   ILE I 232 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ILE I 232 " --> pdb=" O   THR I 217 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AE2
    Processing sheet with id=AE3, first strand: chain 'I' and resid 276 through 277
    Processing sheet with id=AE4, first strand: chain 'I' and resid 316 through 317
      removed outlier: 3.506A  pdb=" N   PHE B 380 " --> pdb=" O   GLU B 396 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLU B 396 " --> pdb=" O   PHE B 380 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'I' and resid 335 through 336
      removed outlier: 6.762A  pdb=" N   GLU I 335 " --> pdb=" O   ALA I 456 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AE5
    Processing sheet with id=AE6, first strand: chain 'I' and resid 345 through 348
      removed outlier: 3.548A  pdb=" N   SER I 348 " --> pdb=" O   GLY I 351 " (cutoff:3.500A)
    Processing sheet with id=AE7, first strand: chain 'I' and resid 377 through 380
    Processing sheet with id=AE8, first strand: chain 'I' and resid 429 through 430
      removed outlier: 3.529A  pdb=" N   SER B 348 " --> pdb=" O   GLY B 351 " (cutoff:3.500A)
    Processing sheet with id=AE9, first strand: chain 'I' and resid 463 through 464
      removed outlier: 4.120A  pdb=" N   TYR I 464 " --> pdb=" O   GLU I 574 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLU I 574 " --> pdb=" O   TYR I 464 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AE9
    Processing sheet with id=AF1, first strand: chain 'I' and resid 470 through 472
      removed outlier: 6.717A  pdb=" N   ASP I 471 " --> pdb=" O   CYS I 490 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AF1
    Processing sheet with id=AF2, first strand: chain 'C' and resid 62 through 72
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 62 through 72
    current: chain 'C' and resid 164 through 167
  No H-bonds generated for sheet with id=AF2
    Processing sheet with id=AF3, first strand: chain 'C' and resid 80 through 84
    Processing sheet with id=AF4, first strand: chain 'C' and resid 216 through 218
      removed outlier: 3.714A  pdb=" N   THR C 217 " --> pdb=" O   ILE C 232 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ILE C 232 " --> pdb=" O   THR C 217 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AF4
    Processing sheet with id=AF5, first strand: chain 'C' and resid 470 through 471
    Processing sheet with id=AF6, first strand: chain 'B' and resid 49 through 53
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 58 through 72
    current: chain 'B' and resid 164 through 167
    Processing sheet with id=AF7, first strand: chain 'B' and resid 80 through 84
    Processing sheet with id=AF8, first strand: chain 'B' and resid 215 through 218
      removed outlier: 6.698A  pdb=" N   ASP B 215 " --> pdb=" O   HIS B 234 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE B 232 " --> pdb=" O   THR B 217 " (cutoff:3.500A)
    Processing sheet with id=AF9, first strand: chain 'B' and resid 276 through 278
    Processing sheet with id=AG1, first strand: chain 'B' and resid 335 through 336
      removed outlier: 6.548A  pdb=" N   GLU B 335 " --> pdb=" O   ALA B 456 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AG1
    Processing sheet with id=AG2, first strand: chain 'B' and resid 415 through 416
    Processing sheet with id=AG3, first strand: chain 'B' and resid 470 through 472
      removed outlier: 6.832A  pdb=" N   ASP B 471 " --> pdb=" O   CYS B 490 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AG3

    295 hydrogen bonds defined for protein.
    567 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 6.06

  Time building geometry restraints manager: 8.89 seconds

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

  Histogram of bond lengths:
        1.20 -     1.34: 10111
        1.34 -     1.48: 8893
        1.48 -     1.63: 12721
        1.63 -     1.77: 1
        1.77 -     1.91: 203
  Bond restraints: 31929
  Sorted by residual:
  bond pdb=" C   LEU A 422 "
       pdb=" N   PRO A 423 "
    ideal  model  delta    sigma   weight residual
    1.333  1.374 -0.041 1.20e-02 6.94e+03 1.18e+01
  bond pdb=" CB  CYS E 490 "
       pdb=" SG  CYS E 490 "
    ideal  model  delta    sigma   weight residual
    1.808  1.907 -0.099 3.30e-02 9.18e+02 9.01e+00
  bond pdb=" CA  ASN I 505 "
       pdb=" CB  ASN I 505 "
    ideal  model  delta    sigma   weight residual
    1.526  1.570 -0.044 1.53e-02 4.27e+03 8.15e+00
  bond pdb=" CB  LYS I 501 "
       pdb=" CG  LYS I 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.605 -0.085 3.00e-02 1.11e+03 8.06e+00
  bond pdb=" C   TYR E 409 "
       pdb=" N   PRO E 410 "
    ideal  model  delta    sigma   weight residual
    1.335  1.372 -0.037 1.30e-02 5.92e+03 7.99e+00
  ... (remaining 31924 not shown)

  Histogram of bond angle deviations from ideal:
       96.84 -   104.36: 723
      104.36 -   111.89: 14121
      111.89 -   119.41: 11856
      119.41 -   126.94: 16324
      126.94 -   134.46: 636
  Bond angle restraints: 43660
  Sorted by residual:
  angle pdb=" CA  PRO E 187 "
        pdb=" N   PRO E 187 "
        pdb=" CD  PRO E 187 "
      ideal   model   delta    sigma   weight residual
     112.00   98.11   13.89 1.40e+00 5.10e-01 9.84e+01
  angle pdb=" CA  CYS E 494 "
        pdb=" CB  CYS E 494 "
        pdb=" SG  CYS E 494 "
      ideal   model   delta    sigma   weight residual
     114.40  127.09  -12.69 2.30e+00 1.89e-01 3.04e+01
  angle pdb=" CA  CYS A 494 "
        pdb=" CB  CYS A 494 "
        pdb=" SG  CYS A 494 "
      ideal   model   delta    sigma   weight residual
     114.40  126.98  -12.58 2.30e+00 1.89e-01 2.99e+01
  angle pdb=" CA  GLN I 213 "
        pdb=" CB  GLN I 213 "
        pdb=" CG  GLN I 213 "
      ideal   model   delta    sigma   weight residual
     114.10  124.49  -10.39 2.00e+00 2.50e-01 2.70e+01
  angle pdb=" CB  GLN F 213 "
        pdb=" CG  GLN F 213 "
        pdb=" CD  GLN F 213 "
      ideal   model   delta    sigma   weight residual
     112.60  121.16   -8.56 1.70e+00 3.46e-01 2.54e+01
  ... (remaining 43655 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 16486
       17.96 -    35.92: 1698
       35.92 -    53.87: 383
       53.87 -    71.83: 66
       71.83 -    89.79: 41
  Dihedral angle restraints: 18674
    sinusoidal: 7165
      harmonic: 11509
  Sorted by residual:
  dihedral pdb=" CA  ASN F 426 "
           pdb=" C   ASN F 426 "
           pdb=" N   ASP F 427 "
           pdb=" CA  ASP F 427 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  142.59   37.41     0      5.00e+00 4.00e-02 5.60e+01
  dihedral pdb=" CB  CYS B 490 "
           pdb=" SG  CYS B 490 "
           pdb=" SG  CYS B 494 "
           pdb=" CB  CYS B 494 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   41.23   51.77     1      1.00e+01 1.00e-02 3.66e+01
  dihedral pdb=" CA  ASN A 493 "
           pdb=" C   ASN A 493 "
           pdb=" N   CYS A 494 "
           pdb=" CA  CYS A 494 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -149.80  -30.20     0      5.00e+00 4.00e-02 3.65e+01
  ... (remaining 18671 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 4078
       0.077 -    0.154: 629
       0.154 -    0.231: 52
       0.231 -    0.307: 2
       0.307 -    0.384: 3
  Chirality restraints: 4764
  Sorted by residual:
  chirality pdb=" CB  ILE D 204 "
            pdb=" CA  ILE D 204 "
            pdb=" CG1 ILE D 204 "
            pdb=" CG2 ILE D 204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.38 2.00e-01 2.50e+01 3.69e+00
  chirality pdb=" CA  SER G 226 "
            pdb=" N   SER G 226 "
            pdb=" C   SER G 226 "
            pdb=" CB  SER G 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.19e+00
  chirality pdb=" CA  ASN F 428 "
            pdb=" N   ASN F 428 "
            pdb=" C   ASN F 428 "
            pdb=" CB  ASN F 428 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.94e+00
  ... (remaining 4761 not shown)

  Planarity restraints: 5732
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR E 186 "   -0.127 5.00e-02 4.00e+02   1.80e-01 5.21e+01
        pdb=" N   PRO E 187 "    0.311 5.00e-02 4.00e+02
        pdb=" CA  PRO E 187 "   -0.103 5.00e-02 4.00e+02
        pdb=" CD  PRO E 187 "   -0.082 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 464 "   -0.026 2.00e-02 2.50e+03   4.08e-02 3.33e+01
        pdb=" CG  TYR E 464 "    0.098 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 464 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 464 "   -0.040 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 464 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 464 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 464 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR E 464 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E 237 "   -0.073 5.00e-02 4.00e+02   1.08e-01 1.87e+01
        pdb=" N   PRO E 238 "    0.187 5.00e-02 4.00e+02
        pdb=" CA  PRO E 238 "   -0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO E 238 "   -0.059 5.00e-02 4.00e+02
  ... (remaining 5729 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 564
        2.64 -     3.21: 28791
        3.21 -     3.77: 46841
        3.77 -     4.34: 65177
        4.34 -     4.90: 107423
  Nonbonded interactions: 248796
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 524 "
            pdb=" O   LEU B 506 "
     model   vdw
     2.076 2.440
  nonbonded pdb=" OG1 THR D  42 "
            pdb=" OE1 GLU D 260 "
     model   vdw
     2.091 2.440
  nonbonded pdb=" O   LEU A 506 "
            pdb=" OH  TYR E 524 "
     model   vdw
     2.096 2.440
  nonbonded pdb=" O   THR F 245 "
            pdb=" OG  SER F 249 "
     model   vdw
     2.101 2.440
  nonbonded pdb=" O   VAL D 149 "
            pdb=" OG  SER D 525 "
     model   vdw
     2.121 2.440
  ... (remaining 248791 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 38 through 294 or resid 299 through 584))
  selection = (chain 'B' and resid 38 through 584)
  selection = (chain 'E' and (resid 38 through 294 or resid 299 through 584))
  selection = (chain 'F' and (resid 38 through 294 or resid 299 through 584))
  selection = (chain 'G' and (resid 38 through 294 or resid 299 through 584))
  selection = (chain 'I' and (resid 38 through 294 or resid 299 through 584))
}
ncs_group {
  reference = (chain 'H' and resid 10 through 108)
  selection = chain 'L'
}

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 group one per residue
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:             0.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.020
  Extract box with map and model:          3.410
  Check model and map are aligned:         0.450
  Set scattering table:                    0.230
  Process input model:                     54.380
  Find NCS groups from input model:        1.380
  Set up NCS constraints:                  0.090
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   62.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
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      :  0.007   0.109  31929  Z= 0.449
  Angle     :  1.104  13.885  43660  Z= 0.591
  Chirality :  0.055   0.384   4764
  Planarity :  0.009   0.180   5732
  Dihedral  : 15.953  89.791  11229
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  3.83 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  : 24.76 %
    Favored  : 74.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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: -1.38 (0.13), residues: 3686
  helix: -2.35 (0.41), residues: 92
  sheet: -1.04 (0.17), residues: 859
  loop : -0.84 (0.11), residues: 2735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.039   0.002   TRP F 109 
   HIS   0.020   0.002   HIS F 102 
   PHE   0.068   0.004   PHE E 243 
   TYR   0.098   0.003   TYR E 464 
   ARG   0.017   0.002   ARG F 481 

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

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

  7372 Ramachandran restraints generated.
    3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7372 Ramachandran restraints generated.
    3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1544 residues out of total 3295 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 1530
  time to evaluate  : 3.688 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 14
  outliers final: 5
  residues processed: 1534
  average time/residue: 0.4666
  time to fit residues: 1110.1731
Evaluate side-chains
  1503 residues out of total 3295 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 1498
  time to evaluate  : 3.459 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.4466
  time to fit residues: 8.1675
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 392
   random chunks:
   chunk 331 optimal weight:    0.0070
   chunk 297 optimal weight:    6.9990
   chunk 164 optimal weight:    0.9990
   chunk 101 optimal weight:    6.9990
   chunk 200 optimal weight:    2.9990
   chunk 158 optimal weight:   10.0000
   chunk 307 optimal weight:    2.9990
   chunk 118 optimal weight:    6.9990
   chunk 186 optimal weight:    0.9980
   chunk 228 optimal weight:    9.9990
   chunk 355 optimal weight:    2.9990
   overall best weight:    1.6004

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

Flipped N/Q/H residues before XYZ refinement:
A 234 HIS
A 277 HIS
A 302 ASN
A 426 ASN
A 491 GLN
** A 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 558 GLN
** G 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 127 GLN
** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 350 GLN
G 468 GLN
F  93 ASN
F 143 GLN
F 234 HIS
** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 497 GLN
** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 565 ASN
D 517 ASN
E  48 GLN
E 143 GLN
E 403 HIS
** E 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 543 HIS
** I 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 383 GLN
** I 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 493 ASN
** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 549 GLN

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
moved from start:          0.1354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.086  31929  Z= 0.196
  Angle     :  0.601   8.711  43660  Z= 0.304
  Chirality :  0.044   0.251   4764
  Planarity :  0.005   0.105   5732
  Dihedral  :  5.643  70.415   4237
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 22.34 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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: -0.87 (0.13), residues: 3686
  helix: -1.47 (0.46), residues: 100
  sheet: -0.61 (0.17), residues: 882
  loop : -0.52 (0.12), residues: 2704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.029   0.002   TRP G 109 
   HIS   0.009   0.001   HIS F 403 
   PHE   0.027   0.002   PHE A 197 
   TYR   0.028   0.001   TYR A 561 
   ARG   0.006   0.001   ARG B 332 

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

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

  7372 Ramachandran restraints generated.
    3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7372 Ramachandran restraints generated.
    3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1653 residues out of total 3295 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 122
    poor density    : 1531
  time to evaluate  : 3.737 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 122
  outliers final: 78
  residues processed: 1562
  average time/residue: 0.4682
  time to fit residues: 1134.9057
Evaluate side-chains
  1568 residues out of total 3295 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 78
    poor density    : 1490
  time to evaluate  : 3.393 
Switching outliers to nearest non-outliers
  outliers start: 78
  outliers final: 0
  residues processed: 78
  average time/residue: 0.3161
  time to fit residues: 48.9444
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 392
   random chunks:
   chunk 197 optimal weight:    1.9990
   chunk 110 optimal weight:    0.0060
   chunk 296 optimal weight:    0.0270
   chunk 242 optimal weight:   10.0000
   chunk 98 optimal weight:    9.9990
   chunk 356 optimal weight:    0.9980
   chunk 385 optimal weight:    1.9990
   chunk 317 optimal weight:    6.9990
   chunk 353 optimal weight:   10.0000
   chunk 121 optimal weight:   10.0000
   chunk 286 optimal weight:    9.9990
   overall best weight:    1.0058

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

Flipped N/Q/H residues before XYZ refinement:
A 282 ASN
A 384 HIS
A 416 GLN
A 426 ASN
** G 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 137 HIS
G 350 GLN
G 468 GLN
G 497 GLN
F 143 GLN
F 166 ASN
** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  72 ASN
** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 166 ASN
E 403 HIS
** E 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 558 GLN
I  48 GLN
I 318 GLN
I 446 ASN
I 483 HIS
** I 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 102 HIS
C 147 ASN
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  31929  Z= 0.162
  Angle     :  0.576  11.929  43660  Z= 0.288
  Chirality :  0.043   0.184   4764
  Planarity :  0.005   0.072   5732
  Dihedral  :  5.185  69.307   4237
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 24.76 %
    Favored  : 73.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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: -0.67 (0.13), residues: 3686
  helix: -0.96 (0.51), residues: 94
  sheet: -0.39 (0.17), residues: 890
  loop : -0.42 (0.12), residues: 2702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.028   0.001   TRP F 109 
   HIS   0.008   0.001   HIS F 403 
   PHE   0.030   0.002   PHE A 266 
   TYR   0.021   0.001   TYR B 510 
   ARG   0.008   0.001   ARG A  67 

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

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

  7372 Ramachandran restraints generated.
    3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7372 Ramachandran restraints generated.
    3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1576 residues out of total 3295 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 72
    poor density    : 1504
  time to evaluate  : 3.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 72
  outliers final: 35
  residues processed: 1525
  average time/residue: 0.4733
  time to fit residues: 1124.4427
Evaluate side-chains
  1523 residues out of total 3295 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 1488
  time to evaluate  : 3.483 
Switching outliers to nearest non-outliers
  outliers start: 35
  outliers final: 0
  residues processed: 35
  average time/residue: 0.3088
  time to fit residues: 24.6325
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 392
   random chunks:
   chunk 352 optimal weight:    0.6980
   chunk 268 optimal weight:    9.9990
   chunk 185 optimal weight:   10.0000
   chunk 39 optimal weight:    7.9990
   chunk 170 optimal weight:    0.9990
   chunk 239 optimal weight:    8.9990
   chunk 357 optimal weight:    0.9980
   chunk 378 optimal weight:    0.8980
   chunk 186 optimal weight:    9.9990
   chunk 339 optimal weight:   10.0000
   chunk 102 optimal weight:   10.0000
   overall best weight:    2.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 497 GLN
G 350 GLN
** G 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 497 GLN
F  95 ASN
** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 143 GLN
** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  72 ASN
** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 403 HIS
** E 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 558 GLN
I  48 GLN
I 416 GLN
** I 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  46 ASN
** C  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
moved from start:          0.2170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  31929  Z= 0.231
  Angle     :  0.584  10.707  43660  Z= 0.294
  Chirality :  0.043   0.181   4764
  Planarity :  0.005   0.062   5732
  Dihedral  :  5.059  68.190   4237
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 26.40 %
    Favored  : 70.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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: -0.60 (0.13), residues: 3686
  helix: -1.08 (0.48), residues: 100
  sheet: -0.30 (0.17), residues: 871
  loop : -0.38 (0.12), residues: 2715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.029   0.002   TRP C 528 
   HIS   0.006   0.001   HIS F 403 
   PHE   0.035   0.002   PHE G 266 
   TYR   0.027   0.002   TYR A 210 
   ARG   0.008   0.001   ARG G  67 

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

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

  7372 Ramachandran restraints generated.
    3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7372 Ramachandran restraints generated.
    3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1633 residues out of total 3295 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 98
    poor density    : 1535
  time to evaluate  : 3.606 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 98
  outliers final: 65
  residues processed: 1564
  average time/residue: 0.4866
  time to fit residues: 1182.5851
Evaluate side-chains
  1569 residues out of total 3295 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 65
    poor density    : 1504
  time to evaluate  : 3.168 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 65
  outliers final: 1
  residues processed: 65
  average time/residue: 0.3014
  time to fit residues: 39.5648
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 392
   random chunks:
   chunk 315 optimal weight:   10.0000
   chunk 215 optimal weight:   10.0000
   chunk 5 optimal weight:    0.0570
   chunk 282 optimal weight:    2.9990
   chunk 156 optimal weight:    6.9990
   chunk 323 optimal weight:    7.9990
   chunk 261 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 193 optimal weight:    9.9990
   chunk 340 optimal weight:   20.0000
   chunk 95 optimal weight:    9.9990
   overall best weight:    4.8106

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 277 HIS
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 181 ASN
** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 403 HIS
G 491 GLN
** F 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 143 GLN
** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  72 ASN
** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 280 GLN
I 383 GLN
I 446 ASN
C  46 ASN
** C  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 102 HIS
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 565 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7173
moved from start:          0.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.098  31929  Z= 0.413
  Angle     :  0.658  10.984  43660  Z= 0.340
  Chirality :  0.047   0.360   4764
  Planarity :  0.005   0.059   5732
  Dihedral  :  5.427  69.013   4237
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 27.37 %
    Favored  : 69.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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: -0.72 (0.13), residues: 3686
  helix: -1.37 (0.41), residues: 124
  sheet: -0.49 (0.17), residues: 919
  loop : -0.39 (0.12), residues: 2643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.042   0.003   TRP F 109 
   HIS   0.008   0.001   HIS A 222 
   PHE   0.036   0.002   PHE A 266 
   TYR   0.029   0.002   TYR A 561 
   ARG   0.009   0.001   ARG G  67 

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

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

  7372 Ramachandran restraints generated.
    3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7372 Ramachandran restraints generated.
    3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1628 residues out of total 3295 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 99
    poor density    : 1529
  time to evaluate  : 3.616 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 99
  outliers final: 60
  residues processed: 1557
  average time/residue: 0.4916
  time to fit residues: 1198.0438
Evaluate side-chains
  1565 residues out of total 3295 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 1505
  time to evaluate  : 3.858 
Switching outliers to nearest non-outliers
  outliers start: 60
  outliers final: 0
  residues processed: 60
  average time/residue: 0.3245
  time to fit residues: 39.9930
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 392
   random chunks:
   chunk 127 optimal weight:    9.9990
   chunk 341 optimal weight:    9.9990
   chunk 74 optimal weight:    2.9990
   chunk 222 optimal weight:    6.9990
   chunk 93 optimal weight:    7.9990
   chunk 379 optimal weight:    7.9990
   chunk 314 optimal weight:    8.9990
   chunk 175 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   chunk 125 optimal weight:    8.9990
   chunk 199 optimal weight:    4.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 137 HIS
A 167 ASN
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 549 GLN
A 558 GLN
G 127 GLN
** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 403 HIS
F 143 GLN
** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 321 ASN
** F 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 497 GLN
** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 280 GLN
I 104 GLN
I 234 HIS
I 446 ASN
** C  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 446 ASN
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 483 HIS
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.2780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.107  31929  Z= 0.436
  Angle     :  0.679   9.858  43660  Z= 0.351
  Chirality :  0.047   0.242   4764
  Planarity :  0.006   0.093   5732
  Dihedral  :  5.580  70.975   4237
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 13.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 29.59 %
    Favored  : 67.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

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: -0.87 (0.13), residues: 3686
  helix: -1.45 (0.40), residues: 124
  sheet: -0.58 (0.17), residues: 926
  loop : -0.51 (0.12), residues: 2636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.063   0.003   TRP G 109 
   HIS   0.007   0.001   HIS F 222 
   PHE   0.036   0.002   PHE A 266 
   TYR   0.036   0.002   TYR A 561 
   ARG   0.009   0.001   ARG F 191 

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

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

  7372 Ramachandran restraints generated.
    3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7372 Ramachandran restraints generated.
    3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1627 residues out of total 3295 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 86
    poor density    : 1541
  time to evaluate  : 3.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 86
  outliers final: 48
  residues processed: 1561
  average time/residue: 0.4730
  time to fit residues: 1147.4244
Evaluate side-chains
  1567 residues out of total 3295 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 1519
  time to evaluate  : 3.529 
Switching outliers to nearest non-outliers
  outliers start: 48
  outliers final: 0
  residues processed: 48
  average time/residue: 0.3300
  time to fit residues: 33.3917
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 392
   random chunks:
   chunk 365 optimal weight:    9.9990
   chunk 42 optimal weight:    0.0980
   chunk 216 optimal weight:    0.9990
   chunk 276 optimal weight:    5.9990
   chunk 214 optimal weight:    6.9990
   chunk 319 optimal weight:    8.9990
   chunk 211 optimal weight:    5.9990
   chunk 377 optimal weight:    0.8980
   chunk 236 optimal weight:    0.0770
   chunk 230 optimal weight:    7.9990
   chunk 174 optimal weight:    1.9990
   overall best weight:    0.8142

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

Flipped N/Q/H residues before XYZ refinement:
A 318 GLN
A 458 ASN
** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 127 GLN
G 280 GLN
** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 375 ASN
G 384 HIS
G 403 HIS
F 143 GLN
** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 497 GLN
** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 143 GLN
** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 104 GLN
I 383 GLN
I 386 GLN
C 181 ASN
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 550 GLN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7119
moved from start:          0.2886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  31929  Z= 0.170
  Angle     :  0.616  10.567  43660  Z= 0.312
  Chirality :  0.043   0.214   4764
  Planarity :  0.005   0.058   5732
  Dihedral  :  5.116  70.838   4237
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 31.32 %
    Favored  : 66.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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 (0.13), residues: 3686
  helix: -1.33 (0.46), residues: 100
  sheet: -0.17 (0.18), residues: 870
  loop : -0.39 (0.12), residues: 2716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.047   0.002   TRP G 528 
   HIS   0.007   0.001   HIS G 222 
   PHE   0.041   0.002   PHE E 266 
   TYR   0.040   0.001   TYR E 464 
   ARG   0.013   0.001   ARG A  67 

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

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

  7372 Ramachandran restraints generated.
    3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7372 Ramachandran restraints generated.
    3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1576 residues out of total 3295 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 59
    poor density    : 1517
  time to evaluate  : 3.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 59
  outliers final: 30
  residues processed: 1534
  average time/residue: 0.4777
  time to fit residues: 1137.7544
Evaluate side-chains
  1514 residues out of total 3295 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 1484
  time to evaluate  : 3.516 
Switching outliers to nearest non-outliers
  outliers start: 30
  outliers final: 0
  residues processed: 30
  average time/residue: 0.3020
  time to fit residues: 21.5961
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 392
   random chunks:
   chunk 233 optimal weight:    0.4980
   chunk 150 optimal weight:    8.9990
   chunk 225 optimal weight:    2.9990
   chunk 113 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 240 optimal weight:    6.9990
   chunk 257 optimal weight:    3.9990
   chunk 186 optimal weight:    2.9990
   chunk 35 optimal weight:    7.9990
   chunk 296 optimal weight:    3.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 231 ASN
** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 384 HIS
G 386 GLN
G 403 HIS
G 497 GLN
** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 466 ASN
** F 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 546 ASN
** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 143 GLN
** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 104 GLN
C  46 ASN
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 222 HIS
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7128
moved from start:          0.3030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  31929  Z= 0.212
  Angle     :  0.633  14.476  43660  Z= 0.318
  Chirality :  0.044   0.192   4764
  Planarity :  0.005   0.053   5732
  Dihedral  :  5.065  68.828   4237
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 32.11 %
    Favored  : 66.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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 (0.14), residues: 3686
  helix: -1.45 (0.42), residues: 124
  sheet: -0.14 (0.18), residues: 881
  loop : -0.38 (0.12), residues: 2681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.055   0.002   TRP G 109 
   HIS   0.004   0.001   HIS B 234 
   PHE   0.031   0.002   PHE F 353 
   TYR   0.039   0.002   TYR A 561 
   ARG   0.009   0.001   ARG A  67 

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

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

  7372 Ramachandran restraints generated.
    3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7372 Ramachandran restraints generated.
    3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1555 residues out of total 3295 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 1495
  time to evaluate  : 3.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 60
  outliers final: 34
  residues processed: 1504
  average time/residue: 0.4815
  time to fit residues: 1127.2418
Evaluate side-chains
  1511 residues out of total 3295 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 1477
  time to evaluate  : 3.415 
Switching outliers to nearest non-outliers
  outliers start: 34
  outliers final: 0
  residues processed: 34
  average time/residue: 0.3347
  time to fit residues: 25.4413
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 392
   random chunks:
   chunk 343 optimal weight:    7.9990
   chunk 361 optimal weight:    9.9990
   chunk 330 optimal weight:   20.0000
   chunk 352 optimal weight:   10.0000
   chunk 211 optimal weight:    7.9990
   chunk 153 optimal weight:   10.0000
   chunk 276 optimal weight:   10.0000
   chunk 108 optimal weight:    6.9990
   chunk 318 optimal weight:    9.9990
   chunk 332 optimal weight:   20.0000
   chunk 350 optimal weight:    7.9990
   overall best weight:    8.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 416 GLN
A 458 ASN
A 468 GLN
G  78 ASN
** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 143 GLN
G 181 ASN
G 231 ASN
** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 386 GLN
G 403 HIS
** G 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  95 ASN
** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 167 ASN
** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 386 GLN
F 421 ASN
F 497 GLN
** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 426 ASN
** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 104 GLN
I 222 HIS
I 318 GLN
I 383 GLN
I 446 ASN
** I 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  46 ASN
** C  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 497 GLN
** B  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7218
moved from start:          0.3308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.161  31929  Z= 0.672
  Angle     :  0.836  16.070  43660  Z= 0.435
  Chirality :  0.053   0.297   4764
  Planarity :  0.007   0.089   5732
  Dihedral  :  6.045  72.669   4237
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 18.59
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  5.67 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 32.72 %
    Favored  : 65.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

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 (0.13), residues: 3686
  helix: -1.68 (0.40), residues: 124
  sheet: -0.32 (0.18), residues: 856
  loop : -0.80 (0.12), residues: 2706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.066   0.004   TRP G 109 
   HIS   0.011   0.002   HIS A 222 
   PHE   0.052   0.003   PHE G  53 
   TYR   0.052   0.003   TYR A 211 
   ARG   0.017   0.001   ARG A  67 

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

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

  7372 Ramachandran restraints generated.
    3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7372 Ramachandran restraints generated.
    3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1569 residues out of total 3295 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 55
    poor density    : 1514
  time to evaluate  : 3.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 55
  outliers final: 39
  residues processed: 1530
  average time/residue: 0.4825
  time to fit residues: 1150.3972
Evaluate side-chains
  1541 residues out of total 3295 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 1502
  time to evaluate  : 3.411 
Switching outliers to nearest non-outliers
  outliers start: 39
  outliers final: 0
  residues processed: 39
  average time/residue: 0.3248
  time to fit residues: 27.2643
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 392
   random chunks:
   chunk 231 optimal weight:    0.0050
   chunk 372 optimal weight:    0.9980
   chunk 227 optimal weight:    0.8980
   chunk 176 optimal weight:    7.9990
   chunk 258 optimal weight:    0.6980
   chunk 390 optimal weight:    0.0970
   chunk 359 optimal weight:    0.5980
   chunk 310 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 240 optimal weight:   10.0000
   chunk 190 optimal weight:    0.1980
   overall best weight:    0.3192

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

Flipped N/Q/H residues before XYZ refinement:
A 302 ASN
** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 497 GLN
G 127 GLN
** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 497 GLN
F 137 HIS
** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 386 GLN
** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 497 GLN
F 546 ASN
** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  48 GLN
I 104 GLN
I 318 GLN
B 115 ASN
B 468 GLN
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.3348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  31929  Z= 0.186
  Angle     :  0.696  15.740  43660  Z= 0.349
  Chirality :  0.045   0.342   4764
  Planarity :  0.005   0.071   5732
  Dihedral  :  5.395  73.320   4237
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 34.26 %
    Favored  : 64.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    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: -0.70 (0.13), residues: 3686
  helix: -1.61 (0.42), residues: 120
  sheet: -0.12 (0.18), residues: 862
  loop : -0.52 (0.12), residues: 2704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.064   0.003   TRP C 528 
   HIS   0.006   0.001   HIS F 222 
   PHE   0.036   0.002   PHE F 448 
   TYR   0.043   0.002   TYR E 464 
   ARG   0.012   0.001   ARG E 382 

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

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

  7372 Ramachandran restraints generated.
    3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  7372 Ramachandran restraints generated.
    3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1528 residues out of total 3295 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 1501
  time to evaluate  : 3.922 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 27
  outliers final: 16
  residues processed: 1504
  average time/residue: 0.4929
  time to fit residues: 1152.9002
Evaluate side-chains
  1484 residues out of total 3295 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 1468
  time to evaluate  : 3.411 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 0
  residues processed: 16
  average time/residue: 0.3198
  time to fit residues: 13.9176
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 392
   random chunks:
   chunk 247 optimal weight:    8.9990
   chunk 331 optimal weight:   30.0000
   chunk 95 optimal weight:   10.0000
   chunk 286 optimal weight:    9.9990
   chunk 45 optimal weight:    9.9990
   chunk 86 optimal weight:    0.9980
   chunk 311 optimal weight:   20.0000
   chunk 130 optimal weight:   10.0000
   chunk 319 optimal weight:    8.9990
   chunk 39 optimal weight:    0.8980
   chunk 57 optimal weight:   20.0000
   overall best weight:    5.9786

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

Flipped N/Q/H residues before XYZ refinement:
** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 143 GLN
** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 403 HIS
** G 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 242 GLN
** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 386 GLN
** F 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 497 GLN
** F 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  64 ASN
** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 565 ASN
** I 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  46 ASN
C  86 ASN
** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.125010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.107108 restraints weight = 52477.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.111325 restraints weight = 24610.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.114066 restraints weight = 13839.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
moved from start:          0.3485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.113  31929  Z= 0.506
  Angle     :  0.794  15.338  43660  Z= 0.408
  Chirality :  0.050   0.270   4764
  Planarity :  0.006   0.097   5732
  Dihedral  :  5.823  73.998   4237
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 18.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 35.02 %
    Favored  : 63.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

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: -0.98 (0.13), residues: 3686
  helix: -1.79 (0.39), residues: 124
  sheet: -0.24 (0.18), residues: 824
  loop : -0.75 (0.12), residues: 2738

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.065   0.004   TRP G 109 
   HIS   0.007   0.001   HIS A  70 
   PHE   0.053   0.003   PHE A 527 
   TYR   0.066   0.003   TYR E 464 
   ARG   0.018   0.001   ARG I 332 

===============================================================================
Job complete
usr+sys time: 14423.98 seconds
wall clock time: 271 minutes 21.41 seconds (16281.41 seconds total)