Starting phenix.real_space_refine
on Fri Feb 16 22:01:32 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5s_11647/02_2024/7a5s_11647.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5s_11647/02_2024/7a5s_11647.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5s_11647/02_2024/7a5s_11647.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5s_11647/02_2024/7a5s_11647.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5s_11647/02_2024/7a5s_11647.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a5s_11647/02_2024/7a5s_11647.pdb"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.027
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      68      5.16       5
     C   10580      2.51       5
     N    2748      2.21       5
     O    3212      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "H GLU   16": "OE1" <-> "OE2"
    Residue "H TYR   27": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H GLU   46": "OE1" <-> "OE2"
    Residue "H TYR   52": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H ASP   55": "OD1" <-> "OD2"
    Residue "H TYR   60": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H PHE   64": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR   80": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H ASP  148": "OD1" <-> "OD2"
    Residue "H PHE  150": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H GLU  152": "OE1" <-> "OE2"
    Residue "H TYR  180": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR  198": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H ASP  212": "OD1" <-> "OD2"
    Residue "H GLU  216": "OE1" <-> "OE2"
    Residue "L ASP    1": "OD1" <-> "OD2"
    Residue "L ASP    9": "OD1" <-> "OD2"
    Residue "L GLU   17": "OE1" <-> "OE2"
    Residue "L TYR   31": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L ARG   60": "NH1" <-> "NH2"
    Residue "L ASP   66": "OD1" <-> "OD2"
    Residue "L PHE   68": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L ASP   76": "OD1" <-> "OD2"
    Residue "L PHE   77": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L GLU   87": "OE1" <-> "OE2"
    Residue "L ASP   88": "OD1" <-> "OD2"
    Residue "L TYR  102": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L GLU  111": "OE1" <-> "OE2"
    Residue "L PHE  122": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L GLU  129": "OE1" <-> "OE2"
    Residue "L TYR  146": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L GLU  171": "OE1" <-> "OE2"
    Residue "L ASP  176": "OD1" <-> "OD2"
    Residue "L TYR  179": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L TYR  192": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L TYR  198": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L PHE  215": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR   38": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP   40": "OD1" <-> "OD2"
    Residue "A PHE   43": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   58": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   65": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   86": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  140": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  145": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  157": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  160": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  168": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  194": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  200": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  220": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  238": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  248": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  265": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  275": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  279": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  306": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  313": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  318": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  351": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  369": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  380": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  392": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  400": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  405": "OD1" <-> "OD2"
    Residue "A ASP  420": "OD1" <-> "OD2"
    Residue "A ASP  427": "OD1" <-> "OD2"
    Residue "A ASP  442": "OD1" <-> "OD2"
    Residue "A PHE  456": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  465": "OE1" <-> "OE2"
    Residue "A ASP  467": "OD1" <-> "OD2"
    Residue "A GLU  516": "OE1" <-> "OE2"
    Residue "A PHE  559": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  565": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  574": "OD1" <-> "OD2"
    Residue "A GLU  583": "OE1" <-> "OE2"
    Residue "A PHE  592": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  636": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  674": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M ASP    1": "OD1" <-> "OD2"
    Residue "M ASP    9": "OD1" <-> "OD2"
    Residue "M GLU   17": "OE1" <-> "OE2"
    Residue "M TYR   31": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M ARG   60": "NH1" <-> "NH2"
    Residue "M ASP   66": "OD1" <-> "OD2"
    Residue "M PHE   68": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M ASP   76": "OD1" <-> "OD2"
    Residue "M PHE   77": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M GLU   87": "OE1" <-> "OE2"
    Residue "M ASP   88": "OD1" <-> "OD2"
    Residue "M TYR  102": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M GLU  111": "OE1" <-> "OE2"
    Residue "M PHE  122": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M GLU  129": "OE1" <-> "OE2"
    Residue "M TYR  146": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M GLU  171": "OE1" <-> "OE2"
    Residue "M ASP  176": "OD1" <-> "OD2"
    Residue "M TYR  179": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M TYR  192": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M TYR  198": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M PHE  215": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   38": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP   40": "OD1" <-> "OD2"
    Residue "B PHE   43": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   58": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   65": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   86": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  135": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  140": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  145": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  157": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  160": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  168": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  194": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  200": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  220": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  238": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  248": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  265": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  275": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  279": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  306": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  313": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  318": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  351": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  369": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  380": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  392": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  400": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  405": "OD1" <-> "OD2"
    Residue "B ASP  420": "OD1" <-> "OD2"
    Residue "B ASP  427": "OD1" <-> "OD2"
    Residue "B ASP  442": "OD1" <-> "OD2"
    Residue "B PHE  456": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  465": "OE1" <-> "OE2"
    Residue "B ASP  467": "OD1" <-> "OD2"
    Residue "B GLU  516": "OE1" <-> "OE2"
    Residue "B PHE  559": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  565": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  574": "OD1" <-> "OD2"
    Residue "B GLU  583": "OE1" <-> "OE2"
    Residue "B PHE  592": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  636": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  674": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I GLU   16": "OE1" <-> "OE2"
    Residue "I TYR   27": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I GLU   46": "OE1" <-> "OE2"
    Residue "I TYR   52": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I ASP   55": "OD1" <-> "OD2"
    Residue "I TYR   60": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I PHE   64": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR   80": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I ASP  148": "OD1" <-> "OD2"
    Residue "I PHE  150": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I GLU  152": "OE1" <-> "OE2"
    Residue "I TYR  180": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I TYR  198": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I ASP  212": "OD1" <-> "OD2"
    Residue "I GLU  216": "OE1" <-> "OE2"
  Time to flip residues: 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 16608
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "H"
      Number of atoms: 1634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1634
          Classifications: {'peptide': 220}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 205}
    Chain: "L"
      Number of atoms: 1694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1694
          Classifications: {'peptide': 218}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206}
    Chain: "A"
      Number of atoms: 4948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 624, 4948
          Classifications: {'peptide': 624}
          Link IDs: {'PTRANS': 31, 'TRANS': 592}
          Chain breaks: 2
    Chain: "M"
      Number of atoms: 1694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1694
          Classifications: {'peptide': 218}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206}
    Chain: "B"
      Number of atoms: 4948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 624, 4948
          Classifications: {'peptide': 624}
          Link IDs: {'PTRANS': 31, 'TRANS': 592}
          Chain breaks: 2
    Chain: "I"
      Number of atoms: 1634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1634
          Classifications: {'peptide': 220}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 205}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 8.83, per 1000 atoms: 0.53
  Number of scatterers: 16608
  At special positions: 0
  Unit cell: (183.703, 190.225, 94.569, 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      68     16.00
     O    3212      8.00
     N    2748      7.00
     C   10580      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=26, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 144 " - pdb=" SG  CYS H 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 140 " - pdb=" SG  CYS L 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 590 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 617 " - pdb=" SG  CYS A 649 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 662 " - pdb=" SG  CYS A 671 " distance=2.04
    Simple disulfide: pdb=" SG  CYS M  23 " - pdb=" SG  CYS M  94 " distance=2.04
    Simple disulfide: pdb=" SG  CYS M 140 " - pdb=" SG  CYS M 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 166 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 538 " - pdb=" SG  CYS B 590 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 617 " - pdb=" SG  CYS B 649 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 662 " - pdb=" SG  CYS B 671 " distance=2.04
    Simple disulfide: pdb=" SG  CYS I  22 " - pdb=" SG  CYS I  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 144 " - pdb=" SG  CYS I 200 " distance=2.04

  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
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG G   1 " - " NAG G   2 "
    NAG-ASN
      " NAG D   1 " - " ASN A 343 "
      " NAG G   1 " - " ASN B 343 "
  Time building additional restraints: 5.99
  Conformation dependent library (CDL) restraints added in 3.0 seconds
  

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3932

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 40 sheets defined
      5.8% alpha, 34.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.59
  Creating SS restraints...
    Processing helix  chain 'H' and resid 160 through 162
      No H-bonds generated for 'chain 'H' and resid 160 through 162'
    Processing helix  chain 'L' and resid 127 through 134
      removed outlier: 3.689A  pdb=" N   LEU L 131 " --> pdb=" O   SER L 127 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LYS L 132 " --> pdb=" O   ASP L 128 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER L 133 " --> pdb=" O   GLU L 129 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLY L 134 " --> pdb=" O   GLN L 130 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 127 through 134'
    Processing helix  chain 'L' and resid 189 through 193
    Processing helix  chain 'A' and resid 294 through 304
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 365 through 369
      removed outlier: 3.964A  pdb=" N   LEU A 368 " --> pdb=" O   TYR A 365 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   TYR A 369 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 365 through 369'
    Processing helix  chain 'A' and resid 383 through 388
      removed outlier: 4.237A  pdb=" N   ASN A 388 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 3.759A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 422
    Processing helix  chain 'A' and resid 438 through 443
      removed outlier: 3.783A  pdb=" N   ASP A 442 " --> pdb=" O   SER A 438 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 127 through 134
      removed outlier: 3.690A  pdb=" N   LEU M 131 " --> pdb=" O   SER M 127 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LYS M 132 " --> pdb=" O   ASP M 128 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER M 133 " --> pdb=" O   GLU M 129 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLY M 134 " --> pdb=" O   GLN M 130 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'M' and resid 127 through 134'
    Processing helix  chain 'M' and resid 189 through 193
    Processing helix  chain 'B' and resid 294 through 304
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 365 through 369
      removed outlier: 3.965A  pdb=" N   LEU B 368 " --> pdb=" O   TYR B 365 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   TYR B 369 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 365 through 369'
    Processing helix  chain 'B' and resid 383 through 388
      removed outlier: 4.237A  pdb=" N   ASN B 388 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 3.759A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.783A  pdb=" N   ASP B 442 " --> pdb=" O   SER B 438 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 160 through 162
      No H-bonds generated for 'chain 'I' and resid 160 through 162'
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11
      removed outlier: 3.749A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 114 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR H 116 " --> pdb=" O   GLU H  10 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.556A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11
      removed outlier: 3.749A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 114 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR H 116 " --> pdb=" O   GLU H  10 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   VAL H 108 " --> pdb=" O   GLY H  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 124 through 128
      removed outlier: 4.342A  pdb=" N   GLY H 143 " --> pdb=" O   LEU H 128 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   CYS H 144 " --> pdb=" O   SER H 184 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER H 184 " --> pdb=" O   CYS H 144 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ASP H 148 " --> pdb=" O   TYR H 180 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   TYR H 180 " --> pdb=" O   ASP H 148 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 155 through 158
      removed outlier: 4.747A  pdb=" N   TYR H 198 " --> pdb=" O   VAL H 215 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.247A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 111 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 30 through 31
      removed outlier: 3.772A  pdb=" N   LYS L  36 " --> pdb=" O   TYR L  31 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 120 through 124
      removed outlier: 3.879A  pdb=" N   SER L 120 " --> pdb=" O   ASN L 143 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ASN L 143 " --> pdb=" O   SER L 120 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 159 through 160
      removed outlier: 3.637A  pdb=" N   TYR L 198 " --> pdb=" O   PHE L 215 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 49 through 55
      removed outlier: 3.512A  pdb=" N   HIS A  49 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU A 277 " --> pdb=" O   HIS A  49 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLN A 271 " --> pdb=" O   PHE A  55 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 63 through 67
      removed outlier: 4.369A  pdb=" N   LYS A 187 " --> pdb=" O   ILE A 210 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   SER A 205 " --> pdb=" O   PRO A 225 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 83 through 85
      removed outlier: 3.838A  pdb=" N   PHE A 168 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 151 through 163
      removed outlier: 6.522A  pdb=" N   SER A 151 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   TYR A 144 " --> pdb=" O   SER A 151 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   MET A 153 " --> pdb=" O   GLY A 142 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   GLY A 142 " --> pdb=" O   MET A 153 " (cutoff:3.500A)
      removed outlier: 9.300A  pdb=" N   SER A 155 " --> pdb=" O   PHE A 140 " (cutoff:3.500A)
      removed outlier: 11.347A  pdb=" N   PHE A 140 " --> pdb=" O   SER A 155 " (cutoff:3.500A)
      removed outlier: 9.837A  pdb=" N   PHE A 157 " --> pdb=" O   ASP A 138 " (cutoff:3.500A)
      removed outlier: 11.223A  pdb=" N   ASP A 138 " --> pdb=" O   PHE A 157 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   VAL A 159 " --> pdb=" O   CYS A 136 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   GLN A 134 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 311 through 313
      removed outlier: 3.569A  pdb=" N   GLY A 311 " --> pdb=" O   THR A 599 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 324 through 328
      removed outlier: 3.761A  pdb=" N   VAL A 539 " --> pdb=" O   GLY A 550 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   THR A 588 " --> pdb=" O   VAL A 551 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   THR A 553 " --> pdb=" O   ASP A 586 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ASP A 586 " --> pdb=" O   THR A 553 " (cutoff:3.500A)
      removed outlier: 5.192A  pdb=" N   ASP A 574 " --> pdb=" O   ILE A 587 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   GLY A 566 " --> pdb=" O   ASP A 574 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.912A  pdb=" N   ILE A 358 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 4.907A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 4.906A  pdb=" N   GLU A 516 " --> pdb=" O   ASN A 394 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ALA A 435 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AC1, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AC2, first strand: chain 'A' and resid 664 through 667
      removed outlier: 6.263A  pdb=" N   ILE A 670 " --> pdb=" O   ILE A 666 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'M' and resid 4 through 7
    Processing sheet with id=AC4, first strand: chain 'M' and resid 10 through 13
      removed outlier: 6.247A  pdb=" N   LEU M  11 " --> pdb=" O   GLU M 111 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   TRP M  41 " --> pdb=" O   LEU M  53 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'M' and resid 30 through 31
      removed outlier: 3.773A  pdb=" N   LYS M  36 " --> pdb=" O   TYR M  31 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'M' and resid 120 through 124
      removed outlier: 3.879A  pdb=" N   SER M 120 " --> pdb=" O   ASN M 143 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ASN M 143 " --> pdb=" O   SER M 120 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'M' and resid 159 through 160
      removed outlier: 3.637A  pdb=" N   TYR M 198 " --> pdb=" O   PHE M 215 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 49 through 55
      removed outlier: 3.512A  pdb=" N   HIS B  49 " --> pdb=" O   LEU B 277 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU B 277 " --> pdb=" O   HIS B  49 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLN B 271 " --> pdb=" O   PHE B  55 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ASP B 287 " --> pdb=" O   LYS B 278 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 63 through 67
      removed outlier: 4.368A  pdb=" N   LYS B 187 " --> pdb=" O   ILE B 210 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   SER B 205 " --> pdb=" O   PRO B 225 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'B' and resid 83 through 85
      removed outlier: 3.838A  pdb=" N   PHE B 168 " --> pdb=" O   VAL B 130 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 151 through 163
      removed outlier: 6.522A  pdb=" N   SER B 151 " --> pdb=" O   TYR B 144 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   TYR B 144 " --> pdb=" O   SER B 151 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   MET B 153 " --> pdb=" O   GLY B 142 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   GLY B 142 " --> pdb=" O   MET B 153 " (cutoff:3.500A)
      removed outlier: 9.300A  pdb=" N   SER B 155 " --> pdb=" O   PHE B 140 " (cutoff:3.500A)
      removed outlier: 11.347A  pdb=" N   PHE B 140 " --> pdb=" O   SER B 155 " (cutoff:3.500A)
      removed outlier: 9.838A  pdb=" N   PHE B 157 " --> pdb=" O   ASP B 138 " (cutoff:3.500A)
      removed outlier: 11.224A  pdb=" N   ASP B 138 " --> pdb=" O   PHE B 157 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   VAL B 159 " --> pdb=" O   CYS B 136 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   GLN B 134 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'B' and resid 311 through 313
      removed outlier: 3.569A  pdb=" N   GLY B 311 " --> pdb=" O   THR B 599 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'B' and resid 324 through 328
      removed outlier: 3.761A  pdb=" N   VAL B 539 " --> pdb=" O   GLY B 550 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   THR B 588 " --> pdb=" O   VAL B 551 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   THR B 553 " --> pdb=" O   ASP B 586 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ASP B 586 " --> pdb=" O   THR B 553 " (cutoff:3.500A)
      removed outlier: 5.192A  pdb=" N   ASP B 574 " --> pdb=" O   ILE B 587 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   GLY B 566 " --> pdb=" O   ASP B 574 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.912A  pdb=" N   ILE B 358 " --> pdb=" O   VAL B 395 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 4.907A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 4.907A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ALA B 435 " --> pdb=" O   THR B 376 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AD7, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AD8, first strand: chain 'B' and resid 664 through 667
      removed outlier: 6.264A  pdb=" N   ILE B 670 " --> pdb=" O   ILE B 666 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'I' and resid 3 through 6
    Processing sheet with id=AE1, first strand: chain 'I' and resid 10 through 11
      removed outlier: 3.749A  pdb=" N   GLU I  10 " --> pdb=" O   THR I 114 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR I 116 " --> pdb=" O   GLU I  10 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLY I  49 " --> pdb=" O   TRP I  36 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ARG I  38 " --> pdb=" O   TRP I  47 " (cutoff:3.500A)
      removed outlier: 5.556A  pdb=" N   TRP I  47 " --> pdb=" O   ARG I  38 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'I' and resid 10 through 11
      removed outlier: 3.749A  pdb=" N   GLU I  10 " --> pdb=" O   THR I 114 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR I 116 " --> pdb=" O   GLU I  10 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   VAL I 108 " --> pdb=" O   GLY I  98 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'I' and resid 124 through 128
      removed outlier: 4.343A  pdb=" N   GLY I 143 " --> pdb=" O   LEU I 128 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   CYS I 144 " --> pdb=" O   SER I 184 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER I 184 " --> pdb=" O   CYS I 144 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ASP I 148 " --> pdb=" O   TYR I 180 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   TYR I 180 " --> pdb=" O   ASP I 148 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'I' and resid 155 through 158
      removed outlier: 4.747A  pdb=" N   TYR I 198 " --> pdb=" O   VAL I 215 " (cutoff:3.500A)

    528 hydrogen bonds defined for protein.
    1344 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: 10.13

  Time building geometry restraints manager: 6.54 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 4594
        1.33 -     1.46: 3725
        1.46 -     1.58: 8629
        1.58 -     1.70: 0
        1.70 -     1.82: 80
  Bond restraints: 17028
  Sorted by residual:
  bond pdb=" N   VAL B 595 "
       pdb=" CA  VAL B 595 "
    ideal  model  delta    sigma   weight residual
    1.456  1.497 -0.040 1.14e-02 7.69e+03 1.25e+01
  bond pdb=" N   VAL A 595 "
       pdb=" CA  VAL A 595 "
    ideal  model  delta    sigma   weight residual
    1.456  1.497 -0.040 1.14e-02 7.69e+03 1.24e+01
  bond pdb=" N   VAL A 534 "
       pdb=" CA  VAL A 534 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.039 1.15e-02 7.56e+03 1.13e+01
  bond pdb=" N   VAL B 534 "
       pdb=" CA  VAL B 534 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.038 1.15e-02 7.56e+03 1.11e+01
  bond pdb=" N   VAL B 551 "
       pdb=" CA  VAL B 551 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.22e-02 6.72e+03 1.07e+01
  ... (remaining 17023 not shown)

  Histogram of bond angle deviations from ideal:
       99.77 -   106.62: 554
      106.62 -   113.46: 9028
      113.46 -   120.30: 6162
      120.30 -   127.15: 7240
      127.15 -   133.99: 188
  Bond angle restraints: 23172
  Sorted by residual:
  angle pdb=" N   PRO A 217 "
        pdb=" CA  PRO A 217 "
        pdb=" C   PRO A 217 "
      ideal   model   delta    sigma   weight residual
     111.22  116.86   -5.64 1.40e+00 5.10e-01 1.62e+01
  angle pdb=" N   PRO B 217 "
        pdb=" CA  PRO B 217 "
        pdb=" C   PRO B 217 "
      ideal   model   delta    sigma   weight residual
     111.22  116.86   -5.64 1.40e+00 5.10e-01 1.62e+01
  angle pdb=" N   ASN B 536 "
        pdb=" CA  ASN B 536 "
        pdb=" C   ASN B 536 "
      ideal   model   delta    sigma   weight residual
     111.74  117.02   -5.28 1.35e+00 5.49e-01 1.53e+01
  angle pdb=" N   ASN A 536 "
        pdb=" CA  ASN A 536 "
        pdb=" C   ASN A 536 "
      ideal   model   delta    sigma   weight residual
     111.74  117.02   -5.28 1.35e+00 5.49e-01 1.53e+01
  angle pdb=" CA  GLY B 268 "
        pdb=" C   GLY B 268 "
        pdb=" O   GLY B 268 "
      ideal   model   delta    sigma   weight residual
     121.76  117.78    3.98 1.03e+00 9.43e-01 1.49e+01
  ... (remaining 23167 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.03: 9283
       18.03 -    36.07: 661
       36.07 -    54.10: 162
       54.10 -    72.14: 30
       72.14 -    90.17: 10
  Dihedral angle restraints: 10146
    sinusoidal: 3986
      harmonic: 6160
  Sorted by residual:
  dihedral pdb=" CB  CYS B 538 "
           pdb=" SG  CYS B 538 "
           pdb=" SG  CYS B 590 "
           pdb=" CB  CYS B 590 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -176.17   90.17     1      1.00e+01 1.00e-02 9.63e+01
  dihedral pdb=" CB  CYS A 538 "
           pdb=" SG  CYS A 538 "
           pdb=" SG  CYS A 590 "
           pdb=" CB  CYS A 590 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -176.14   90.14     1      1.00e+01 1.00e-02 9.62e+01
  dihedral pdb=" C   ASP A 578 "
           pdb=" N   ASP A 578 "
           pdb=" CA  ASP A 578 "
           pdb=" CB  ASP A 578 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.80   11.20     0      2.50e+00 1.60e-01 2.01e+01
  ... (remaining 10143 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 2015
       0.069 -    0.137: 474
       0.137 -    0.206: 61
       0.206 -    0.275: 20
       0.275 -    0.343: 6
  Chirality restraints: 2576
  Sorted by residual:
  chirality pdb=" CA  ASN B 536 "
            pdb=" N   ASN B 536 "
            pdb=" C   ASN B 536 "
            pdb=" CB  ASN B 536 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.95e+00
  chirality pdb=" CA  ASN A 536 "
            pdb=" N   ASN A 536 "
            pdb=" C   ASN A 536 "
            pdb=" CB  ASN A 536 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.94e+00
  chirality pdb=" CA  ASP A 578 "
            pdb=" N   ASP A 578 "
            pdb=" C   ASP A 578 "
            pdb=" CB  ASP A 578 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.80e+00
  ... (remaining 2573 not shown)

  Planarity restraints: 2976
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 548 "   -0.018 2.00e-02 2.50e+03   3.54e-02 1.25e+01
        pdb=" C   GLY B 548 "    0.061 2.00e-02 2.50e+03
        pdb=" O   GLY B 548 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   THR B 549 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 548 "    0.018 2.00e-02 2.50e+03   3.51e-02 1.23e+01
        pdb=" C   GLY A 548 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   GLY A 548 "    0.023 2.00e-02 2.50e+03
        pdb=" N   THR A 549 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 571 "   -0.013 2.00e-02 2.50e+03   2.61e-02 6.81e+00
        pdb=" C   ASP A 571 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ASP A 571 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   THR A 572 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 2973 not shown)

  Histogram of nonbonded interaction distances:
        1.19 -     1.93: 6
        1.93 -     2.67: 277
        2.67 -     3.42: 20398
        3.42 -     4.16: 36938
        4.16 -     4.90: 65913
  Nonbonded interactions: 123532
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG B 273 "
            pdb=" OD2 ASP B 290 "
     model   vdw
     1.188 2.520
  nonbonded pdb=" NH2 ARG A 273 "
            pdb=" OD2 ASP A 290 "
     model   vdw
     1.189 2.520
  nonbonded pdb=" NH2 ARG A 273 "
            pdb=" CG  ASP A 290 "
     model   vdw
     1.373 3.350
  nonbonded pdb=" NH2 ARG B 273 "
            pdb=" CG  ASP B 290 "
     model   vdw
     1.373 3.350
  nonbonded pdb=" NH2 ARG A 273 "
            pdb=" OD1 ASP A 290 "
     model   vdw
     1.766 2.520
  ... (remaining 123527 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'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'H'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'L'
  selection = chain 'M'
}

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:             2.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          14.120
  Check model and map are aligned:         0.320
  Set scattering table:                    0.220
  Process input model:                     52.960
  Find NCS groups from input model:        1.250
  Set up NCS constraints:                  0.140
  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:             0.010
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   74.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6684
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      :  0.006   0.041  17028  Z= 0.392
  Angle     :  0.931   8.725  23172  Z= 0.569
  Chirality :  0.062   0.343   2576
  Planarity :  0.005   0.051   2974
  Dihedral  : 13.403  89.368   6136
  Min Nonbonded Distance : 1.188

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  6.94 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  5.66 %
    Favored  : 93.70 %
  Cbeta Deviations :  0.20 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    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: -2.00 (0.17), residues: 2104
  helix: -2.03 (0.51), residues: 88
  sheet:  0.09 (0.20), residues: 698
  loop : -2.23 (0.15), residues: 1318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP H  83 
 HIS   0.010   0.001   HIS L 195 
 PHE   0.017   0.002   PHE H  29 
 TYR   0.019   0.002   TYR B 351 
 ARG   0.006   0.001   ARG B 328 

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 200
  time to evaluate  : 1.996 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 MET cc_start: -0.2022 (ttm) cc_final: -0.4005 (mtp)
REVERT: B  177 MET cc_start: -0.1960 (ttm) cc_final: -0.3964 (mtp)
  outliers start: 12
  outliers final: 2
  residues processed: 208
  average time/residue: 0.3487
  time to fit residues: 103.3024
Evaluate side-chains
  92 residues out of total 1856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 90
  time to evaluate  : 1.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 177 optimal weight:    2.9990
   chunk 159 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9990
   chunk 54 optimal weight:   30.0000
   chunk 107 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0870
   chunk 164 optimal weight:    1.9990
   chunk 63 optimal weight:    8.9990
   chunk 100 optimal weight:    0.8980
   chunk 122 optimal weight:    3.9990
   chunk 190 optimal weight:    4.9990
   overall best weight:    1.3964

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

Flipped N/Q/H residues before XYZ refinement:
H   1 GLN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
H  77 ASN
L  44 GLN
L  95 GLN
L 106 GLN
A  66 HIS
A 115 GLN
A 146 HIS
A 164 ASN
A 218 GLN
A 239 GLN
A 245 HIS
A 271 GLN
A 321 GLN
A 542 ASN
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 613 GLN
A 641 ASN
A 658 ASN
M  44 GLN
M  95 GLN
M 106 GLN
B  66 HIS
B 115 GLN
B 146 HIS
B 164 ASN
B 218 GLN
B 239 GLN
B 245 HIS
B 271 GLN
B 321 GLN
B 370 ASN
B 542 ASN
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 613 GLN
B 641 ASN
B 658 ASN
** I   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  39 GLN
I  77 ASN

Total number of N/Q/H flips: 38

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6881
moved from start:          0.2435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  17028  Z= 0.294
  Angle     :  0.695   7.060  23172  Z= 0.364
  Chirality :  0.047   0.145   2576
  Planarity :  0.005   0.039   2974
  Dihedral  :  5.792  49.834   2380
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.28 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 10.40 %
    Favored  : 87.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.17), residues: 2104
  helix: -2.08 (0.56), residues: 86
  sheet:  0.36 (0.19), residues: 750
  loop : -2.09 (0.15), residues: 1268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP I  83 
 HIS   0.005   0.001   HIS L 195 
 PHE   0.023   0.002   PHE A  55 
 TYR   0.033   0.002   TYR B 612 
 ARG   0.005   0.001   ARG L  18 

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 104
  time to evaluate  : 1.984 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    2 MET cc_start: 0.7057 (ppp) cc_final: 0.6692 (ttp)
REVERT: H  149 TYR cc_start: 0.8480 (p90) cc_final: 0.8268 (p90)
REVERT: A  177 MET cc_start: -0.1795 (ttm) cc_final: -0.3340 (mtp)
REVERT: I    2 MET cc_start: 0.7521 (ppp) cc_final: 0.6706 (ppp)
  outliers start: 34
  outliers final: 22
  residues processed: 129
  average time/residue: 0.2647
  time to fit residues: 54.6463
Evaluate side-chains
  98 residues out of total 1856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 76
  time to evaluate  : 1.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  201 ASN
Chi-restraints excluded: chain H residue  212 ASP
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  655 HIS
Chi-restraints excluded: chain M residue  195 HIS
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  650 LEU
Chi-restraints excluded: chain B residue  655 HIS
Chi-restraints excluded: chain I residue  104 THR
Chi-restraints excluded: chain I residue  199 ILE
Chi-restraints excluded: chain I residue  201 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 105 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   chunk 158 optimal weight:    0.0570
   chunk 129 optimal weight:    0.8980
   chunk 52 optimal weight:    7.9990
   chunk 191 optimal weight:    2.9990
   chunk 206 optimal weight:    2.9990
   chunk 170 optimal weight:    1.9990
   chunk 189 optimal weight:    2.9990
   chunk 65 optimal weight:   20.0000
   chunk 153 optimal weight:    0.0020
   overall best weight:    0.5306

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

Flipped N/Q/H residues before XYZ refinement:
** H   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 216 ASN
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6850
moved from start:          0.2923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  17028  Z= 0.161
  Angle     :  0.580   6.925  23172  Z= 0.299
  Chirality :  0.044   0.146   2576
  Planarity :  0.004   0.045   2974
  Dihedral  :  5.235  49.977   2380
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.39 %
    Favored  : 85.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.18), residues: 2104
  helix: -2.09 (0.52), residues: 100
  sheet:  0.66 (0.19), residues: 740
  loop : -1.86 (0.16), residues: 1264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP I  83 
 HIS   0.007   0.001   HIS M 195 
 PHE   0.012   0.001   PHE B 133 
 TYR   0.012   0.001   TYR B 204 
 ARG   0.004   0.000   ARG L  18 

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 92
  time to evaluate  : 1.926 
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: H    2 MET cc_start: 0.7041 (ppp) cc_final: 0.6609 (ttp)
REVERT: A  177 MET cc_start: -0.1953 (ttm) cc_final: -0.4403 (mpp)
REVERT: I    2 MET cc_start: 0.7635 (ppp) cc_final: 0.7390 (ttp)
  outliers start: 31
  outliers final: 21
  residues processed: 115
  average time/residue: 0.2543
  time to fit residues: 47.1492
Evaluate side-chains
  103 residues out of total 1856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 1.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  201 ASN
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  655 HIS
Chi-restraints excluded: chain M residue  191 ASP
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  650 LEU
Chi-restraints excluded: chain B residue  655 HIS
Chi-restraints excluded: chain I residue  201 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 188 optimal weight:    3.9990
   chunk 143 optimal weight:    4.9990
   chunk 99 optimal weight:    7.9990
   chunk 21 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9980
   chunk 128 optimal weight:    4.9990
   chunk 191 optimal weight:    2.9990
   chunk 202 optimal weight:    2.9990
   chunk 100 optimal weight:    7.9990
   chunk 181 optimal weight:    2.9990
   chunk 54 optimal weight:   30.0000
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
** H   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   6 GLN
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 321 GLN
A 370 ASN
A 474 GLN
A 493 GLN
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 675 GLN
M   6 GLN
** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 321 GLN
B 474 GLN
B 493 GLN
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 675 GLN
** I   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7081
moved from start:          0.3962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.091  17028  Z= 0.540
  Angle     :  0.772  11.060  23172  Z= 0.406
  Chirality :  0.050   0.188   2576
  Planarity :  0.006   0.072   2974
  Dihedral  :  5.837  51.425   2380
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 13.79 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.17), residues: 2104
  helix: -2.40 (0.52), residues: 88
  sheet:  0.30 (0.18), residues: 742
  loop : -2.01 (0.16), residues: 1274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP H  83 
 HIS   0.006   0.001   HIS M 195 
 PHE   0.031   0.003   PHE I 170 
 TYR   0.020   0.003   TYR H 180 
 ARG   0.004   0.001   ARG M 217 

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 56
    poor density    : 77
  time to evaluate  : 1.937 
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: H  106 MET cc_start: 0.8912 (mtm) cc_final: 0.8531 (mtm)
REVERT: H  107 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8497 (p0)
REVERT: L   31 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.7100 (t80)
REVERT: A  148 ASN cc_start: 0.3604 (OUTLIER) cc_final: 0.3379 (p0)
REVERT: A  177 MET cc_start: -0.1988 (ttm) cc_final: -0.3437 (mmm)
REVERT: A  353 TRP cc_start: 0.8945 (OUTLIER) cc_final: 0.8382 (p-90)
REVERT: M   31 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.6961 (t80)
REVERT: B  177 MET cc_start: -0.2120 (mmt) cc_final: -0.2383 (mmt)
REVERT: B  353 TRP cc_start: 0.8958 (OUTLIER) cc_final: 0.8403 (p-90)
REVERT: I  106 MET cc_start: 0.8920 (mtm) cc_final: 0.8514 (mtm)
REVERT: I  107 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8546 (p0)
REVERT: I  185 VAL cc_start: 0.9170 (OUTLIER) cc_final: 0.8916 (m)
  outliers start: 56
  outliers final: 36
  residues processed: 117
  average time/residue: 0.2542
  time to fit residues: 48.0524
Evaluate side-chains
  114 residues out of total 1856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 70
  time to evaluate  : 1.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue  107 ASP
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  201 ASN
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain L residue  191 ASP
Chi-restraints excluded: chain L residue  215 PHE
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  353 TRP
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  655 HIS
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain M residue  191 ASP
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain B residue  552 LEU
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  655 HIS
Chi-restraints excluded: chain I residue   17 SER
Chi-restraints excluded: chain I residue  107 ASP
Chi-restraints excluded: chain I residue  125 VAL
Chi-restraints excluded: chain I residue  145 LEU
Chi-restraints excluded: chain I residue  173 VAL
Chi-restraints excluded: chain I residue  179 LEU
Chi-restraints excluded: chain I residue  185 VAL
Chi-restraints excluded: chain I residue  201 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 169 optimal weight:    0.9980
   chunk 115 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 151 optimal weight:    7.9990
   chunk 83 optimal weight:    3.9990
   chunk 173 optimal weight:    0.9980
   chunk 140 optimal weight:   30.0000
   chunk 0 optimal weight:    0.5980
   chunk 103 optimal weight:   20.0000
   chunk 182 optimal weight:    9.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    1.4782

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

Flipped N/Q/H residues before XYZ refinement:
** H   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  95 GLN
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 613 GLN
A 675 GLN
M  95 GLN
** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 613 GLN
B 675 GLN
** I   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
moved from start:          0.4075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  17028  Z= 0.282
  Angle     :  0.597   9.219  23172  Z= 0.313
  Chirality :  0.045   0.146   2576
  Planarity :  0.004   0.048   2974
  Dihedral  :  5.435  49.981   2380
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 15.73 %
    Favored  : 81.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.17), residues: 2104
  helix: -2.28 (0.53), residues: 88
  sheet:  0.38 (0.19), residues: 738
  loop : -1.88 (0.16), residues: 1278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP H  83 
 HIS   0.003   0.001   HIS M 195 
 PHE   0.021   0.001   PHE B 168 
 TYR   0.018   0.002   TYR I 180 
 ARG   0.003   0.000   ARG L  18 

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 80
  time to evaluate  : 2.016 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  107 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8540 (p0)
REVERT: H  185 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.8851 (m)
REVERT: L   31 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.7100 (t80)
REVERT: A  148 ASN cc_start: 0.3447 (OUTLIER) cc_final: 0.3188 (p0)
REVERT: A  168 PHE cc_start: 0.2703 (t80) cc_final: 0.2230 (t80)
REVERT: A  177 MET cc_start: -0.1982 (ttm) cc_final: -0.3433 (mmm)
REVERT: A  353 TRP cc_start: 0.8891 (OUTLIER) cc_final: 0.8068 (p-90)
REVERT: M   31 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.7027 (t80)
REVERT: B  177 MET cc_start: -0.2175 (mmt) cc_final: -0.2382 (mmt)
REVERT: B  353 TRP cc_start: 0.8901 (OUTLIER) cc_final: 0.7959 (p-90)
REVERT: I  107 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8505 (p0)
  outliers start: 46
  outliers final: 31
  residues processed: 115
  average time/residue: 0.2672
  time to fit residues: 49.5647
Evaluate side-chains
  110 residues out of total 1856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 71
  time to evaluate  : 1.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  107 ASP
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  185 VAL
Chi-restraints excluded: chain H residue  201 ASN
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain L residue  191 ASP
Chi-restraints excluded: chain L residue  215 PHE
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  353 TRP
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  655 HIS
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue  191 ASP
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  655 HIS
Chi-restraints excluded: chain I residue   17 SER
Chi-restraints excluded: chain I residue   31 THR
Chi-restraints excluded: chain I residue  107 ASP
Chi-restraints excluded: chain I residue  145 LEU
Chi-restraints excluded: chain I residue  173 VAL
Chi-restraints excluded: chain I residue  179 LEU
Chi-restraints excluded: chain I residue  201 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 68 optimal weight:    5.9990
   chunk 182 optimal weight:    0.4980
   chunk 40 optimal weight:    3.9990
   chunk 119 optimal weight:    2.9990
   chunk 50 optimal weight:   10.0000
   chunk 203 optimal weight:    0.9990
   chunk 168 optimal weight:    2.9990
   chunk 94 optimal weight:   10.0000
   chunk 16 optimal weight:    0.7980
   chunk 67 optimal weight:    4.9990
   chunk 106 optimal weight:    5.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7051
moved from start:          0.4310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  17028  Z= 0.316
  Angle     :  0.604   8.411  23172  Z= 0.317
  Chirality :  0.046   0.179   2576
  Planarity :  0.004   0.045   2974
  Dihedral  :  5.202  48.786   2378
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.00 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.17), residues: 2104
  helix: -2.27 (0.53), residues: 88
  sheet:  0.32 (0.19), residues: 748
  loop : -1.86 (0.16), residues: 1268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP H  83 
 HIS   0.004   0.001   HIS M 195 
 PHE   0.013   0.002   PHE B 106 
 TYR   0.018   0.002   TYR I 180 
 ARG   0.002   0.000   ARG L  18 

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 56
    poor density    : 72
  time to evaluate  : 2.039 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  185 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8919 (m)
REVERT: L   31 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.7012 (t80)
REVERT: A  148 ASN cc_start: 0.3569 (OUTLIER) cc_final: 0.3312 (p0)
REVERT: A  177 MET cc_start: -0.2076 (ttm) cc_final: -0.3466 (mmm)
REVERT: A  353 TRP cc_start: 0.8917 (OUTLIER) cc_final: 0.8049 (p-90)
REVERT: M   31 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.7017 (t80)
REVERT: B  177 MET cc_start: -0.2382 (mmt) cc_final: -0.2609 (mmt)
REVERT: B  353 TRP cc_start: 0.8921 (OUTLIER) cc_final: 0.8047 (p-90)
REVERT: I  107 ASP cc_start: 0.8880 (OUTLIER) cc_final: 0.8516 (p0)
  outliers start: 56
  outliers final: 34
  residues processed: 117
  average time/residue: 0.2393
  time to fit residues: 46.4195
Evaluate side-chains
  105 residues out of total 1856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 64
  time to evaluate  : 1.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  183 SER
Chi-restraints excluded: chain H residue  185 VAL
Chi-restraints excluded: chain H residue  201 ASN
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain L residue  191 ASP
Chi-restraints excluded: chain L residue  215 PHE
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  353 TRP
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  655 HIS
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain M residue  191 ASP
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  552 LEU
Chi-restraints excluded: chain B residue  655 HIS
Chi-restraints excluded: chain I residue   17 SER
Chi-restraints excluded: chain I residue   31 THR
Chi-restraints excluded: chain I residue  107 ASP
Chi-restraints excluded: chain I residue  145 LEU
Chi-restraints excluded: chain I residue  173 VAL
Chi-restraints excluded: chain I residue  179 LEU
Chi-restraints excluded: chain I residue  183 SER
Chi-restraints excluded: chain I residue  201 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 195 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 115 optimal weight:    0.4980
   chunk 148 optimal weight:   20.0000
   chunk 114 optimal weight:    0.5980
   chunk 171 optimal weight:    0.9990
   chunk 113 optimal weight:    0.0770
   chunk 202 optimal weight:    0.7980
   chunk 126 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6985
moved from start:          0.4372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  17028  Z= 0.154
  Angle     :  0.537   8.176  23172  Z= 0.280
  Chirality :  0.044   0.145   2576
  Planarity :  0.004   0.041   2974
  Dihedral  :  4.802  44.373   2378
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 16.76 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.17), residues: 2104
  helix: -2.44 (0.48), residues: 100
  sheet:  0.49 (0.19), residues: 722
  loop : -1.74 (0.16), residues: 1282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H  83 
 HIS   0.005   0.001   HIS L 195 
 PHE   0.029   0.001   PHE B 168 
 TYR   0.013   0.001   TYR L  55 
 ARG   0.002   0.000   ARG L  18 

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 81
  time to evaluate  : 2.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  185 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8942 (m)
REVERT: A  148 ASN cc_start: 0.3481 (OUTLIER) cc_final: 0.3221 (p0)
REVERT: A  177 MET cc_start: -0.2139 (ttm) cc_final: -0.3471 (mmm)
REVERT: I    2 MET cc_start: 0.8316 (ppp) cc_final: 0.7231 (ppp)
REVERT: I  107 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8497 (p0)
REVERT: I  145 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8307 (pt)
  outliers start: 37
  outliers final: 24
  residues processed: 109
  average time/residue: 0.2502
  time to fit residues: 44.7423
Evaluate side-chains
  99 residues out of total 1856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 71
  time to evaluate  : 1.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  183 SER
Chi-restraints excluded: chain H residue  185 VAL
Chi-restraints excluded: chain H residue  201 ASN
Chi-restraints excluded: chain L residue  191 ASP
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain M residue  191 ASP
Chi-restraints excluded: chain M residue  216 ASN
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain I residue   31 THR
Chi-restraints excluded: chain I residue  107 ASP
Chi-restraints excluded: chain I residue  145 LEU
Chi-restraints excluded: chain I residue  201 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 125 optimal weight:    7.9990
   chunk 80 optimal weight:    1.9990
   chunk 120 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 128 optimal weight:    0.0060
   chunk 137 optimal weight:   30.0000
   chunk 100 optimal weight:    5.9990
   chunk 18 optimal weight:    0.6980
   chunk 159 optimal weight:    0.9990
   chunk 184 optimal weight:    3.9990
   overall best weight:    0.7198

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

Flipped N/Q/H residues before XYZ refinement:
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 675 GLN
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6991
moved from start:          0.4491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  17028  Z= 0.170
  Angle     :  0.549   9.742  23172  Z= 0.284
  Chirality :  0.045   0.192   2576
  Planarity :  0.004   0.042   2974
  Dihedral  :  4.731  42.541   2378
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.97 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.18), residues: 2104
  helix: -2.41 (0.47), residues: 100
  sheet:  0.50 (0.19), residues: 766
  loop : -1.70 (0.16), residues: 1238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  83 
 HIS   0.005   0.001   HIS L 195 
 PHE   0.010   0.001   PHE A  79 
 TYR   0.015   0.001   TYR H  27 
 ARG   0.004   0.000   ARG A 237 

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 75
  time to evaluate  : 1.836 
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: H    2 MET cc_start: 0.8250 (ppp) cc_final: 0.7266 (ppp)
REVERT: A  148 ASN cc_start: 0.3475 (OUTLIER) cc_final: 0.3210 (p0)
REVERT: A  177 MET cc_start: -0.1912 (ttm) cc_final: -0.3326 (mmm)
REVERT: M   31 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.7067 (t80)
REVERT: B  177 MET cc_start: -0.1995 (mmt) cc_final: -0.2850 (mmt)
REVERT: I    2 MET cc_start: 0.8353 (ppp) cc_final: 0.7239 (ppp)
  outliers start: 38
  outliers final: 30
  residues processed: 106
  average time/residue: 0.2464
  time to fit residues: 43.1351
Evaluate side-chains
  99 residues out of total 1856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 67
  time to evaluate  : 1.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  183 SER
Chi-restraints excluded: chain H residue  201 ASN
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  191 ASP
Chi-restraints excluded: chain L residue  215 PHE
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue  191 ASP
Chi-restraints excluded: chain M residue  216 ASN
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain I residue   31 THR
Chi-restraints excluded: chain I residue  125 VAL
Chi-restraints excluded: chain I residue  183 SER
Chi-restraints excluded: chain I residue  201 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 193 optimal weight:    0.0570
   chunk 176 optimal weight:    0.8980
   chunk 188 optimal weight:    3.9990
   chunk 113 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 148 optimal weight:    6.9990
   chunk 57 optimal weight:   20.0000
   chunk 170 optimal weight:    3.9990
   chunk 178 optimal weight:    0.0050
   chunk 187 optimal weight:    0.0870
   chunk 123 optimal weight:    0.8980
   overall best weight:    0.3890

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

Flipped N/Q/H residues before XYZ refinement:
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 675 GLN
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 196 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6958
moved from start:          0.4573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  17028  Z= 0.132
  Angle     :  0.526   8.516  23172  Z= 0.271
  Chirality :  0.044   0.154   2576
  Planarity :  0.004   0.041   2974
  Dihedral  :  4.483  38.795   2378
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 17.51 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.18), residues: 2104
  helix: -2.18 (0.48), residues: 100
  sheet:  0.67 (0.19), residues: 758
  loop : -1.63 (0.16), residues: 1246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 436 
 HIS   0.003   0.000   HIS L 195 
 PHE   0.035   0.001   PHE B 168 
 TYR   0.013   0.001   TYR L  55 
 ARG   0.004   0.000   ARG A 237 

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 71
  time to evaluate  : 2.049 
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: H    2 MET cc_start: 0.8231 (ppp) cc_final: 0.7193 (ppp)
REVERT: H  107 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8617 (p0)
REVERT: A  148 ASN cc_start: 0.3727 (OUTLIER) cc_final: 0.3456 (p0)
REVERT: A  177 MET cc_start: -0.1688 (ttm) cc_final: -0.3157 (mmm)
REVERT: B  168 PHE cc_start: 0.3012 (t80) cc_final: 0.2154 (t80)
REVERT: B  177 MET cc_start: -0.1913 (mmt) cc_final: -0.3377 (mmt)
REVERT: I    2 MET cc_start: 0.8319 (ppp) cc_final: 0.7240 (ppp)
  outliers start: 31
  outliers final: 25
  residues processed: 98
  average time/residue: 0.2677
  time to fit residues: 42.4871
Evaluate side-chains
  95 residues out of total 1856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 68
  time to evaluate  : 2.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  107 ASP
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  183 SER
Chi-restraints excluded: chain H residue  201 ASN
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  215 PHE
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain M residue  216 ASN
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain I residue  183 SER
Chi-restraints excluded: chain I residue  201 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 199 optimal weight:    2.9990
   chunk 121 optimal weight:    2.9990
   chunk 94 optimal weight:    7.9990
   chunk 138 optimal weight:   10.0000
   chunk 209 optimal weight:    0.9980
   chunk 192 optimal weight:    0.8980
   chunk 166 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 128 optimal weight:    3.9990
   chunk 102 optimal weight:    9.9990
   chunk 132 optimal weight:   10.0000
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
L 153 GLN
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 675 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.4813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  17028  Z= 0.324
  Angle     :  0.602   6.789  23172  Z= 0.316
  Chirality :  0.046   0.249   2576
  Planarity :  0.004   0.043   2974
  Dihedral  :  4.885  42.156   2378
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 17.40 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.18), residues: 2104
  helix: -1.95 (0.52), residues: 88
  sheet:  0.62 (0.19), residues: 714
  loop : -1.80 (0.16), residues: 1302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H  83 
 HIS   0.005   0.001   HIS M 195 
 PHE   0.024   0.002   PHE B 168 
 TYR   0.013   0.002   TYR I 180 
 ARG   0.002   0.000   ARG A 237 

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

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

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4208 Ramachandran restraints generated.
    2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 64
  time to evaluate  : 1.779 
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: H    2 MET cc_start: 0.8419 (ppp) cc_final: 0.7371 (ppp)
REVERT: H  106 MET cc_start: 0.8658 (mtm) cc_final: 0.8391 (mtm)
REVERT: L   31 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.6974 (t80)
REVERT: A  148 ASN cc_start: 0.3674 (OUTLIER) cc_final: 0.3403 (p0)
REVERT: A  177 MET cc_start: -0.1905 (ttm) cc_final: -0.3278 (mmm)
REVERT: A  353 TRP cc_start: 0.8924 (OUTLIER) cc_final: 0.8077 (p-90)
REVERT: M   31 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7062 (t80)
REVERT: B  177 MET cc_start: -0.1862 (mmt) cc_final: -0.3331 (mmt)
REVERT: B  353 TRP cc_start: 0.8930 (OUTLIER) cc_final: 0.8078 (p-90)
REVERT: I    2 MET cc_start: 0.8534 (ppp) cc_final: 0.7419 (ppp)
  outliers start: 37
  outliers final: 29
  residues processed: 95
  average time/residue: 0.2780
  time to fit residues: 42.7121
Evaluate side-chains
  98 residues out of total 1856 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 64
  time to evaluate  : 2.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  183 SER
Chi-restraints excluded: chain H residue  201 ASN
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  215 PHE
Chi-restraints excluded: chain A residue   63 THR
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  200 TYR
Chi-restraints excluded: chain A residue  353 TRP
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue   89 VAL
Chi-restraints excluded: chain M residue  191 ASP
Chi-restraints excluded: chain M residue  216 ASN
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   68 ILE
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  153 MET
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  353 TRP
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  552 LEU
Chi-restraints excluded: chain I residue  125 VAL
Chi-restraints excluded: chain I residue  183 SER
Chi-restraints excluded: chain I residue  201 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 177 optimal weight:   10.0000
   chunk 51 optimal weight:    8.9990
   chunk 153 optimal weight:    6.9990
   chunk 24 optimal weight:    0.3980
   chunk 46 optimal weight:    7.9990
   chunk 166 optimal weight:    2.9990
   chunk 69 optimal weight:   10.0000
   chunk 171 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   chunk 146 optimal weight:    0.5980
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 675 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.098016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.064402 restraints weight = 54538.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.063322 restraints weight = 36881.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.063318 restraints weight = 29646.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.4990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  17028  Z= 0.290
  Angle     :  0.572   6.706  23172  Z= 0.301
  Chirality :  0.045   0.148   2576
  Planarity :  0.004   0.039   2974
  Dihedral  :  4.945  44.019   2378
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 17.67 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.93 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.17), residues: 2104
  helix: -2.34 (0.47), residues: 100
  sheet:  0.58 (0.19), residues: 722
  loop : -1.77 (0.16), residues: 1282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H  83 
 HIS   0.003   0.001   HIS M 195 
 PHE   0.034   0.002   PHE B 168 
 TYR   0.013   0.001   TYR I 180 
 ARG   0.003   0.000   ARG A 237 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2669.61 seconds
wall clock time: 50 minutes 12.19 seconds (3012.19 seconds total)