Starting phenix.real_space_refine
on Sun Jul 21 06:59:31 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp2_41464/07_2024/8tp2_41464.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp2_41464/07_2024/8tp2_41464.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp2_41464/07_2024/8tp2_41464.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp2_41464/07_2024/8tp2_41464.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp2_41464/07_2024/8tp2_41464.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp2_41464/07_2024/8tp2_41464.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      77      5.16       5
     C    8448      2.51       5
     N    2286      2.21       5
     O    2674      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "H TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H PHE   78": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L TYR   36": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L TYR   49": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L PHE   62": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L GLU  105": "OE1" <-> "OE2"
    Residue "C TYR   86": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  102": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  148": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  161": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  195": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  201": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  232": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  258": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  294": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  338": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  351": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  353": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  363": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  399": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  417": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  467": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  468": "OE1" <-> "OE2"
    Residue "C TYR  470": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  491": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  492": "OE1" <-> "OE2"
    Residue "C GLU  493": "OE1" <-> "OE2"
    Residue "A TYR   86": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  102": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  148": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  161": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  195": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  201": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  232": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  258": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  294": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  338": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  351": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  353": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  363": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  399": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  417": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  467": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  470": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  491": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  493": "OE1" <-> "OE2"
    Residue "B GLU   31": "OE1" <-> "OE2"
    Residue "B TYR   86": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  102": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  148": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  161": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  195": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  201": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  232": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  258": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  294": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  338": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  351": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  353": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  363": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  393": "OE1" <-> "OE2"
    Residue "B PHE  399": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  417": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  467": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  468": "OE1" <-> "OE2"
    Residue "B TYR  470": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  491": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  493": "OE1" <-> "OE2"
  Time to flip residues: 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib"
  Total number of atoms: 13485
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "H"
      Number of atoms: 959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 959
          Classifications: {'peptide': 126}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 118}
    Chain: "L"
      Number of atoms: 814
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 814
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100}
    Chain: "C"
      Number of atoms: 3821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 482, 3821
          Classifications: {'peptide': 482}
          Link IDs: {'PTRANS': 19, 'TRANS': 462}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 3816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 481, 3816
          Classifications: {'peptide': 481}
          Link IDs: {'PTRANS': 19, 'TRANS': 461}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 482, 3821
          Classifications: {'peptide': 482}
          Link IDs: {'PTRANS': 19, 'TRANS': 462}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "F"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "B"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 7.08, per 1000 atoms: 0.53
  Number of scatterers: 13485
  At special positions: 0
  Unit cell: (108.1, 94.3, 177.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      77     16.00
     O    2674      8.00
     N    2286      7.00
     C    8448      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=20, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  14 " - pdb=" SG  CYS C 466 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  52 " - pdb=" SG  CYS C 277 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  64 " - pdb=" SG  CYS C  76 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  97 " - pdb=" SG  CYS C 139 " distance=2.06
    Simple disulfide: pdb=" SG  CYS C 281 " - pdb=" SG  CYS C 305 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 473 " - pdb=" SG  CYS C 477 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  14 " - pdb=" SG  CYS A 466 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  52 " - pdb=" SG  CYS A 277 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  64 " - pdb=" SG  CYS A  76 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  97 " - pdb=" SG  CYS A 139 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 281 " - pdb=" SG  CYS A 305 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 473 " - pdb=" SG  CYS A 477 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  14 " - pdb=" SG  CYS B 466 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  52 " - pdb=" SG  CYS B 277 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  64 " - pdb=" SG  CYS B  76 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  97 " - pdb=" SG  CYS B 139 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 281 " - pdb=" SG  CYS B 305 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 473 " - pdb=" SG  CYS B 477 " distance=2.05

  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 E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    BETA1-6
      " NAG D   1 " - " FUC D   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
      " NAG E   1 " - " FUC E   3 "
      " NAG F   1 " - " FUC F   3 "
    NAG-ASN
      " NAG A 501 " - " ASN A  21 "
      " NAG A 502 " - " ASN A  33 "
      " NAG A 503 " - " ASN A 289 "
      " NAG B 501 " - " ASN B  21 "
      " NAG B 502 " - " ASN B  33 "
      " NAG B 503 " - " ASN B 289 "
      " NAG C 501 " - " ASN C  33 "
      " NAG C 502 " - " ASN C 289 "
      " NAG C 503 " - " ASN C 483 "
      " NAG C 504 " - " ASN C  21 "
      " NAG D   1 " - " ASN C 169 "
      " NAG E   1 " - " ASN A 169 "
      " NAG F   1 " - " ASN B 169 "
  Time building additional restraints: 4.64
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3060

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 39 sheets defined
      23.9% alpha, 28.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.82
  Creating SS restraints...
    Processing helix  chain 'H' and resid 61 through 65
      removed outlier: 3.695A  pdb=" N   ARG H  64 " --> pdb=" O   PRO H  61 " (cutoff:3.500A)
      removed outlier: 5.360A  pdb=" N   SER H  65 " --> pdb=" O   SER H  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 61 through 65'
    Processing helix  chain 'L' and resid 79 through 83
    Processing helix  chain 'C' and resid 65 through 72
    Processing helix  chain 'C' and resid 73 through 80
      removed outlier: 3.981A  pdb=" N   ASP C  77 " --> pdb=" O   PRO C  74 " (cutoff:3.500A)
      removed outlier: 5.426A  pdb=" N   ARG C  78 " --> pdb=" O   GLU C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 104 through 112
    Processing helix  chain 'C' and resid 125 through 127
    Processing helix  chain 'C' and resid 187 through 196
    Processing helix  chain 'C' and resid 366 through 387
    Processing helix  chain 'C' and resid 403 through 456
      removed outlier: 3.654A  pdb=" N   GLN C 454 " --> pdb=" O   LYS C 450 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 474 through 483
    Processing helix  chain 'C' and resid 488 through 492
    Processing helix  chain 'A' and resid 65 through 72
    Processing helix  chain 'A' and resid 73 through 80
      removed outlier: 3.960A  pdb=" N   ASP A  77 " --> pdb=" O   PRO A  74 " (cutoff:3.500A)
      removed outlier: 5.397A  pdb=" N   ARG A  78 " --> pdb=" O   GLU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 112
    Processing helix  chain 'A' and resid 125 through 127
    Processing helix  chain 'A' and resid 187 through 196
    Processing helix  chain 'A' and resid 366 through 387
    Processing helix  chain 'A' and resid 403 through 456
      removed outlier: 3.654A  pdb=" N   GLN A 454 " --> pdb=" O   LYS A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 482
      removed outlier: 3.563A  pdb=" N   SER A 480 " --> pdb=" O   GLU A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 491
    Processing helix  chain 'B' and resid 65 through 72
    Processing helix  chain 'B' and resid 73 through 80
      removed outlier: 3.968A  pdb=" N   ASP B  77 " --> pdb=" O   PRO B  74 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   ARG B  78 " --> pdb=" O   GLU B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 112
    Processing helix  chain 'B' and resid 125 through 127
    Processing helix  chain 'B' and resid 187 through 196
    Processing helix  chain 'B' and resid 366 through 387
    Processing helix  chain 'B' and resid 403 through 456
      removed outlier: 3.658A  pdb=" N   GLN B 454 " --> pdb=" O   LYS B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 484
    Processing helix  chain 'B' and resid 487 through 491
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
      removed outlier: 6.168A  pdb=" N   LEU H  18 " --> pdb=" O   THR H  82A" (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   THR H  82A" --> pdb=" O   LEU H  18 " (cutoff:3.500A)
      removed outlier: 7.649A  pdb=" N   LEU H  20 " --> pdb=" O   LYS H  81 " (cutoff:3.500A)
      removed outlier: 5.360A  pdb=" N   LYS H  81 " --> pdb=" O   LEU H  20 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   CYS H  22 " --> pdb=" O   SER H  79 " (cutoff:3.500A)
      removed outlier: 5.538A  pdb=" N   SER H  79 " --> pdb=" O   CYS H  22 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   LEU H  24 " --> pdb=" O   GLN H  77 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   GLN H  77 " --> pdb=" O   LEU H  24 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 5.299A  pdb=" N   TYR H  33 " --> pdb=" O   ASP H  95 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   TRP H  34 " --> pdb=" O   ASN H  50 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   ASN H  50 " --> pdb=" O   TRP H  34 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12
    Processing sheet with id=AA4, first strand: chain 'H' and resid 100B through 100C
      removed outlier: 7.424A  pdb=" N   ALA C 138 " --> pdb=" O   ASN C 144 " (cutoff:3.500A)
      removed outlier: 10.081A  pdb=" N   ASN C 144 " --> pdb=" O   ALA C 138 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 11
      removed outlier: 6.391A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 5.458A  pdb=" N   LYS L  39 " --> pdb=" O   ALA L  43 " (cutoff:3.500A)
      removed outlier: 5.266A  pdb=" N   ALA L  43 " --> pdb=" O   LYS L  39 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 11
    Processing sheet with id=AA8, first strand: chain 'C' and resid 361 through 365
    Processing sheet with id=AA9, first strand: chain 'C' and resid 24 through 26
      removed outlier: 4.310A  pdb=" N   GLU C  24 " --> pdb=" O   VAL C  36 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 39 through 41
    Processing sheet with id=AB2, first strand: chain 'C' and resid 43 through 44
    Processing sheet with id=AB3, first strand: chain 'C' and resid 51 through 54
      removed outlier: 7.059A  pdb=" N   LEU C  51 " --> pdb=" O   GLU C 275 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   CYS C 277 " --> pdb=" O   LEU C  51 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 60
      removed outlier: 6.452A  pdb=" N   LEU C  59 " --> pdb=" O   MET C  88 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   ILE C  87 " --> pdb=" O   MET C 268 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'C' and resid 100 through 102
      removed outlier: 6.505A  pdb=" N   SER C 101 " --> pdb=" O   PHE C 232 " (cutoff:3.500A)
      removed outlier: 8.757A  pdb=" N   TRP C 234 " --> pdb=" O   SER C 101 " (cutoff:3.500A)
      removed outlier: 5.243A  pdb=" N   ILE C 179 " --> pdb=" O   TYR C 256 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   TYR C 256 " --> pdb=" O   ILE C 179 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 100 through 102
      removed outlier: 6.505A  pdb=" N   SER C 101 " --> pdb=" O   PHE C 232 " (cutoff:3.500A)
      removed outlier: 8.757A  pdb=" N   TRP C 234 " --> pdb=" O   SER C 101 " (cutoff:3.500A)
      removed outlier: 7.790A  pdb=" N   ILE C 179 " --> pdb=" O   PRO C 254 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 164 through 169
    Processing sheet with id=AB8, first strand: chain 'C' and resid 286 through 287
    Processing sheet with id=AB9, first strand: chain 'A' and resid 361 through 365
    Processing sheet with id=AC1, first strand: chain 'A' and resid 24 through 26
      removed outlier: 4.197A  pdb=" N   GLU A  24 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 39 through 41
    Processing sheet with id=AC3, first strand: chain 'A' and resid 43 through 44
    Processing sheet with id=AC4, first strand: chain 'A' and resid 51 through 54
      removed outlier: 7.175A  pdb=" N   LEU A  51 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 4.966A  pdb=" N   CYS A 277 " --> pdb=" O   LEU A  51 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'A' and resid 59 through 60
      removed outlier: 6.551A  pdb=" N   LEU A  59 " --> pdb=" O   MET A  88 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   ILE A  87 " --> pdb=" O   MET A 268 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC5
    Processing sheet with id=AC6, first strand: chain 'A' and resid 100 through 102
      removed outlier: 6.478A  pdb=" N   SER A 101 " --> pdb=" O   PHE A 232 " (cutoff:3.500A)
      removed outlier: 8.707A  pdb=" N   TRP A 234 " --> pdb=" O   SER A 101 " (cutoff:3.500A)
      removed outlier: 5.247A  pdb=" N   ILE A 179 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   TYR A 256 " --> pdb=" O   ILE A 179 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'A' and resid 100 through 102
      removed outlier: 6.478A  pdb=" N   SER A 101 " --> pdb=" O   PHE A 232 " (cutoff:3.500A)
      removed outlier: 8.707A  pdb=" N   TRP A 234 " --> pdb=" O   SER A 101 " (cutoff:3.500A)
      removed outlier: 7.806A  pdb=" N   ILE A 179 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'A' and resid 136 through 141
      removed outlier: 7.374A  pdb=" N   ALA A 138 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
      removed outlier: 9.966A  pdb=" N   ASN A 144 " --> pdb=" O   ALA A 138 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'A' and resid 164 through 169
    Processing sheet with id=AD1, first strand: chain 'A' and resid 286 through 287
    Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 365
    Processing sheet with id=AD3, first strand: chain 'B' and resid 24 through 26
      removed outlier: 4.379A  pdb=" N   GLU B  24 " --> pdb=" O   VAL B  36 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'B' and resid 39 through 41
    Processing sheet with id=AD5, first strand: chain 'B' and resid 43 through 44
    Processing sheet with id=AD6, first strand: chain 'B' and resid 51 through 54
      removed outlier: 7.026A  pdb=" N   LEU B  51 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
      removed outlier: 5.121A  pdb=" N   CYS B 277 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'B' and resid 59 through 60
      removed outlier: 6.414A  pdb=" N   LEU B  59 " --> pdb=" O   MET B  88 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   ILE B  87 " --> pdb=" O   MET B 268 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD7
    Processing sheet with id=AD8, first strand: chain 'B' and resid 100 through 102
      removed outlier: 6.506A  pdb=" N   SER B 101 " --> pdb=" O   PHE B 232 " (cutoff:3.500A)
      removed outlier: 8.734A  pdb=" N   TRP B 234 " --> pdb=" O   SER B 101 " (cutoff:3.500A)
      removed outlier: 5.267A  pdb=" N   ILE B 179 " --> pdb=" O   TYR B 256 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   TYR B 256 " --> pdb=" O   ILE B 179 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'B' and resid 100 through 102
      removed outlier: 6.506A  pdb=" N   SER B 101 " --> pdb=" O   PHE B 232 " (cutoff:3.500A)
      removed outlier: 8.734A  pdb=" N   TRP B 234 " --> pdb=" O   SER B 101 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   ILE B 179 " --> pdb=" O   PRO B 254 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'B' and resid 136 through 141
      removed outlier: 7.386A  pdb=" N   ALA B 138 " --> pdb=" O   ASN B 144 " (cutoff:3.500A)
      removed outlier: 9.971A  pdb=" N   ASN B 144 " --> pdb=" O   ALA B 138 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'B' and resid 164 through 169
    Processing sheet with id=AE3, first strand: chain 'B' and resid 286 through 287

    581 hydrogen bonds defined for protein.
    1533 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: 4.31

  Time building geometry restraints manager: 5.12 seconds

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

  Histogram of bond lengths:
        1.18 -     1.32: 2924
        1.32 -     1.46: 4486
        1.46 -     1.59: 6253
        1.59 -     1.73: 15
        1.73 -     1.87: 110
  Bond restraints: 13788
  Sorted by residual:
  bond pdb=" NE1 TRP H  34 "
       pdb=" CE2 TRP H  34 "
    ideal  model  delta    sigma   weight residual
    1.370  1.310  0.060 1.10e-02 8.26e+03 2.95e+01
  bond pdb=" CA  SER B 265 "
       pdb=" CB  SER B 265 "
    ideal  model  delta    sigma   weight residual
    1.542  1.499  0.043 8.90e-03 1.26e+04 2.34e+01
  bond pdb=" CB  HIS C  47 "
       pdb=" CG  HIS C  47 "
    ideal  model  delta    sigma   weight residual
    1.497  1.433  0.064 1.40e-02 5.10e+03 2.12e+01
  bond pdb=" CA  ASN B 322 "
       pdb=" C   ASN B 322 "
    ideal  model  delta    sigma   weight residual
    1.524  1.466  0.058 1.27e-02 6.20e+03 2.08e+01
  bond pdb=" CA  ASN A 322 "
       pdb=" C   ASN A 322 "
    ideal  model  delta    sigma   weight residual
    1.524  1.466  0.058 1.27e-02 6.20e+03 2.07e+01
  ... (remaining 13783 not shown)

  Histogram of bond angle deviations from ideal:
       96.77 -   104.28: 214
      104.28 -   111.79: 5977
      111.79 -   119.30: 5587
      119.30 -   126.81: 6661
      126.81 -   134.32: 236
  Bond angle restraints: 18675
  Sorted by residual:
  angle pdb=" N   THR A 318 "
        pdb=" CA  THR A 318 "
        pdb=" C   THR A 318 "
      ideal   model   delta    sigma   weight residual
     114.04  103.82   10.22 1.24e+00 6.50e-01 6.80e+01
  angle pdb=" C   LYS H  13 "
        pdb=" N   PRO H  14 "
        pdb=" CA  PRO H  14 "
      ideal   model   delta    sigma   weight residual
     119.82  127.90   -8.08 9.80e-01 1.04e+00 6.79e+01
  angle pdb=" C   PRO B  57 "
        pdb=" N   PRO B  58 "
        pdb=" CA  PRO B  58 "
      ideal   model   delta    sigma   weight residual
     120.21  127.92   -7.71 9.60e-01 1.09e+00 6.45e+01
  angle pdb=" C   PRO C  57 "
        pdb=" N   PRO C  58 "
        pdb=" CA  PRO C  58 "
      ideal   model   delta    sigma   weight residual
     120.21  127.81   -7.60 9.60e-01 1.09e+00 6.26e+01
  angle pdb=" N   THR B 318 "
        pdb=" CA  THR B 318 "
        pdb=" C   THR B 318 "
      ideal   model   delta    sigma   weight residual
     114.04  104.27    9.77 1.24e+00 6.50e-01 6.21e+01
  ... (remaining 18670 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.08: 8172
       18.08 -    36.16: 220
       36.16 -    54.24: 37
       54.24 -    72.32: 32
       72.32 -    90.40: 18
  Dihedral angle restraints: 8479
    sinusoidal: 3681
      harmonic: 4798
  Sorted by residual:
  dihedral pdb=" CB  CYS B  64 "
           pdb=" SG  CYS B  64 "
           pdb=" SG  CYS B  76 "
           pdb=" CB  CYS B  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -124.84   38.84     1      1.00e+01 1.00e-02 2.12e+01
  dihedral pdb=" CB  CYS C  64 "
           pdb=" SG  CYS C  64 "
           pdb=" SG  CYS C  76 "
           pdb=" CB  CYS C  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -121.97   35.97     1      1.00e+01 1.00e-02 1.83e+01
  dihedral pdb=" CB  CYS A  64 "
           pdb=" SG  CYS A  64 "
           pdb=" SG  CYS A  76 "
           pdb=" CB  CYS A  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -121.69   35.69     1      1.00e+01 1.00e-02 1.80e+01
  ... (remaining 8476 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 1487
       0.096 -    0.192: 441
       0.192 -    0.289: 97
       0.289 -    0.385: 25
       0.385 -    0.481: 12
  Chirality restraints: 2062
  Sorted by residual:
  chirality pdb=" C1  NAG E   2 "
            pdb=" O4  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.63    0.23 2.00e-02 2.50e+03 1.30e+02
  chirality pdb=" C1  NAG F   2 "
            pdb=" O4  NAG F   1 "
            pdb=" C2  NAG F   2 "
            pdb=" O5  NAG F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.60    0.20 2.00e-02 2.50e+03 9.75e+01
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.59    0.19 2.00e-02 2.50e+03 8.79e+01
  ... (remaining 2059 not shown)

  Planarity restraints: 2412
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C 503 "   -0.349 2.00e-02 2.50e+03   3.01e-01 1.13e+03
        pdb=" C7  NAG C 503 "    0.082 2.00e-02 2.50e+03
        pdb=" C8  NAG C 503 "   -0.112 2.00e-02 2.50e+03
        pdb=" N2  NAG C 503 "    0.537 2.00e-02 2.50e+03
        pdb=" O7  NAG C 503 "   -0.158 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B  21 "    0.072 2.00e-02 2.50e+03   7.64e-02 7.30e+01
        pdb=" CG  ASN B  21 "   -0.030 2.00e-02 2.50e+03
        pdb=" OD1 ASN B  21 "   -0.016 2.00e-02 2.50e+03
        pdb=" ND2 ASN B  21 "   -0.119 2.00e-02 2.50e+03
        pdb=" C1  NAG B 501 "    0.093 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A  21 "    0.064 2.00e-02 2.50e+03   6.82e-02 5.81e+01
        pdb=" CG  ASN A  21 "   -0.025 2.00e-02 2.50e+03
        pdb=" OD1 ASN A  21 "   -0.016 2.00e-02 2.50e+03
        pdb=" ND2 ASN A  21 "   -0.106 2.00e-02 2.50e+03
        pdb=" C1  NAG A 501 "    0.083 2.00e-02 2.50e+03
  ... (remaining 2409 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 83
        2.59 -     3.17: 11168
        3.17 -     3.74: 20349
        3.74 -     4.32: 31035
        4.32 -     4.90: 49663
  Nonbonded interactions: 112298
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP H  95 "
            pdb=" CE1 PHE H 100J"
     model   vdw
     2.009 3.340
  nonbonded pdb=" OG  SER A 136 "
            pdb=" NE2 GLN A 226 "
     model   vdw
     2.116 2.520
  nonbonded pdb=" OG  SER C 136 "
            pdb=" NE2 GLN C 226 "
     model   vdw
     2.164 2.520
  nonbonded pdb=" OG  SER B 136 "
            pdb=" NE2 GLN B 226 "
     model   vdw
     2.257 2.520
  nonbonded pdb=" OD2 ASP B 487 "
            pdb=" NZ  LYS B 490 "
     model   vdw
     2.391 2.520
  ... (remaining 112293 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' and (resid 11 through 324 or resid 335 through 495 or resid 501 throu \ 
gh 503))
  selection = (chain 'C' and (resid 11 through 324 or resid 335 through 495 or resid 501 throu \ 
gh 503))
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     35.010
  Find NCS groups from input model:        0.780
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
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      :  0.021   0.121  13788  Z= 1.344
  Angle     :  1.694  11.265  18675  Z= 1.134
  Chirality :  0.103   0.481   2062
  Planarity :  0.010   0.301   2399
  Dihedral  : 10.562  90.404   5359
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 1.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.19), residues: 1662
  helix:  0.98 (0.26), residues: 335
  sheet:  1.14 (0.25), residues: 388
  loop :  0.18 (0.19), residues: 939

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.007   TRP A  84 
 HIS   0.012   0.003   HIS C 183 
 PHE   0.048   0.006   PHE B 118 
 TYR   0.064   0.008   TYR A 486 
 ARG   0.007   0.001   ARG C  93 

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

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

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  349 residues out of total 1465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 349
  time to evaluate  : 1.655 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   47 TYR cc_start: 0.8848 (t80) cc_final: 0.8641 (t80)
REVERT: L   83 PHE cc_start: 0.7366 (m-80) cc_final: 0.7152 (m-80)
REVERT: L   90 GLN cc_start: 0.8395 (tm130) cc_final: 0.8070 (tm-30)
REVERT: C  435 ARG cc_start: 0.7909 (mmm160) cc_final: 0.7684 (mmp-170)
REVERT: C  441 ASP cc_start: 0.8129 (m-30) cc_final: 0.7924 (m-30)
REVERT: C  445 LYS cc_start: 0.8499 (tptp) cc_final: 0.8231 (ttmm)
REVERT: C  450 LYS cc_start: 0.8961 (tttt) cc_final: 0.8625 (ttpp)
REVERT: A  132 THR cc_start: 0.8426 (p) cc_final: 0.8213 (p)
REVERT: A  160 ASN cc_start: 0.7250 (m-40) cc_final: 0.6810 (t0)
REVERT: A  335 ILE cc_start: 0.6682 (pt) cc_final: 0.6120 (tt)
REVERT: A  402 LEU cc_start: 0.9146 (mt) cc_final: 0.8922 (mt)
REVERT: B   27 ASP cc_start: 0.7654 (m-30) cc_final: 0.7424 (m-30)
REVERT: B  190 GLU cc_start: 0.6994 (tt0) cc_final: 0.6606 (tt0)
REVERT: B  275 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7233 (mp0)
REVERT: B  366 ASP cc_start: 0.8447 (t0) cc_final: 0.8218 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 349
  average time/residue: 0.3132
  time to fit residues: 148.8765
Evaluate side-chains
  173 residues out of total 1465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 1.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 140 optimal weight:    0.8980
   chunk 125 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 84 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9980
   chunk 130 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 96 optimal weight:    3.9990
   chunk 150 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
H   5 GLN
L  92 ASN
C 355 HIS
C 391 GLN
A 196 GLN
A 210 ASN
A 354 HIS
B  12 GLN
B 130 HIS
B 175 GLN
B 183 HIS
B 226 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  13788  Z= 0.240
  Angle     :  0.607   6.213  18675  Z= 0.336
  Chirality :  0.044   0.190   2062
  Planarity :  0.004   0.064   2399
  Dihedral  :  5.550  50.405   2187
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  :  6.55 %
    Favored  : 91.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.20), residues: 1662
  helix:  2.22 (0.28), residues: 333
  sheet:  0.78 (0.26), residues: 380
  loop : -0.23 (0.19), residues: 949

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP L  96 
 HIS   0.012   0.001   HIS C 355 
 PHE   0.024   0.002   PHE C 118 
 TYR   0.018   0.002   TYR B  17 
 ARG   0.004   0.001   ARG A 262a

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

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

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 195
  time to evaluate  : 1.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   92 ASN cc_start: 0.8618 (t0) cc_final: 0.8242 (t0)
REVERT: C  188 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7624 (mt-10)
REVERT: C  435 ARG cc_start: 0.7802 (mmm160) cc_final: 0.7583 (mmp-170)
REVERT: C  445 LYS cc_start: 0.8577 (tptp) cc_final: 0.8217 (ttmm)
REVERT: A   50 LYS cc_start: 0.7893 (mttt) cc_final: 0.7687 (mtpt)
REVERT: A  487 ASP cc_start: 0.7638 (t0) cc_final: 0.7184 (t70)
REVERT: B   27 ASP cc_start: 0.7862 (m-30) cc_final: 0.7611 (m-30)
REVERT: B  239 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7472 (mtm)
REVERT: B  275 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7187 (mp0)
  outliers start: 22
  outliers final: 13
  residues processed: 211
  average time/residue: 0.2985
  time to fit residues: 89.4840
Evaluate side-chains
  171 residues out of total 1465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 157
  time to evaluate  : 1.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   17 THR
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain C residue   11 ASP
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  291 THR
Chi-restraints excluded: chain C residue  355 HIS
Chi-restraints excluded: chain A residue  165 LYS
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  226 GLN
Chi-restraints excluded: chain B residue  239 MET
Chi-restraints excluded: chain B residue  457 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 83 optimal weight:    7.9990
   chunk 46 optimal weight:    0.4980
   chunk 125 optimal weight:    5.9990
   chunk 102 optimal weight:    4.9990
   chunk 41 optimal weight:    0.5980
   chunk 151 optimal weight:    0.7980
   chunk 163 optimal weight:    3.9990
   chunk 134 optimal weight:    2.9990
   chunk 149 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 121 optimal weight:    0.7980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** L  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 117 HIS
A 117 HIS
A 210 ASN
B 117 HIS
B 183 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.3067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  13788  Z= 0.248
  Angle     :  0.545   4.716  18675  Z= 0.298
  Chirality :  0.043   0.228   2062
  Planarity :  0.004   0.057   2399
  Dihedral  :  5.223  58.104   2187
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  7.78 %
    Favored  : 90.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.20), residues: 1662
  helix:  2.32 (0.27), residues: 333
  sheet:  0.66 (0.25), residues: 407
  loop : -0.43 (0.19), residues: 922

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  84 
 HIS   0.027   0.001   HIS C 355 
 PHE   0.031   0.002   PHE C 118 
 TYR   0.015   0.002   TYR L  49 
 ARG   0.003   0.000   ARG A 229 

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

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

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 178
  time to evaluate  : 1.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   92 ASN cc_start: 0.8546 (t0) cc_final: 0.8144 (t0)
REVERT: C  112 LEU cc_start: 0.7935 (mt) cc_final: 0.7674 (mt)
REVERT: C  188 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7647 (mt-10)
REVERT: C  432 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8028 (mm-30)
REVERT: C  435 ARG cc_start: 0.7811 (mmm160) cc_final: 0.7545 (mmp-170)
REVERT: C  445 LYS cc_start: 0.8602 (tptp) cc_final: 0.8150 (ttmm)
REVERT: A  367 LYS cc_start: 0.8111 (mttp) cc_final: 0.7897 (mptt)
REVERT: A  487 ASP cc_start: 0.7541 (t0) cc_final: 0.7191 (t70)
REVERT: B   27 ASP cc_start: 0.7992 (m-30) cc_final: 0.7730 (m-30)
REVERT: B  275 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7128 (mp0)
  outliers start: 23
  outliers final: 20
  residues processed: 191
  average time/residue: 0.2901
  time to fit residues: 77.4151
Evaluate side-chains
  186 residues out of total 1465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 166
  time to evaluate  : 1.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain C residue   11 ASP
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  273 THR
Chi-restraints excluded: chain C residue  291 THR
Chi-restraints excluded: chain A residue  210 ASN
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain B residue  118 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  335 ILE
Chi-restraints excluded: chain B residue  457 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 149 optimal weight:    3.9990
   chunk 113 optimal weight:    4.9990
   chunk 78 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 72 optimal weight:    6.9990
   chunk 101 optimal weight:    2.9990
   chunk 151 optimal weight:    0.9990
   chunk 160 optimal weight:    0.5980
   chunk 79 optimal weight:    1.9990
   chunk 143 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
** L  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 160 ASN
B 183 HIS
B 196 GLN
B 483 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.3433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.077  13788  Z= 0.369
  Angle     :  0.604   7.212  18675  Z= 0.321
  Chirality :  0.045   0.240   2062
  Planarity :  0.004   0.049   2399
  Dihedral  :  5.398  57.478   2187
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  9.15 %
    Favored  : 89.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.20), residues: 1662
  helix:  2.15 (0.27), residues: 333
  sheet:  0.54 (0.26), residues: 405
  loop : -0.60 (0.19), residues: 924

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  84 
 HIS   0.008   0.001   HIS B 117 
 PHE   0.041   0.003   PHE A 118 
 TYR   0.014   0.002   TYR B  17 
 ARG   0.007   0.001   ARG L  61 

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

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

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 164
  time to evaluate  : 1.540 
Fit side-chains
   revert: symmetry clash
REVERT: L   92 ASN cc_start: 0.8643 (t0) cc_final: 0.8262 (t0)
REVERT: C  112 LEU cc_start: 0.8060 (mt) cc_final: 0.7805 (mt)
REVERT: C  188 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7673 (mt-10)
REVERT: C  432 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8018 (mm-30)
REVERT: C  445 LYS cc_start: 0.8628 (tptp) cc_final: 0.8152 (ttmm)
REVERT: A  367 LYS cc_start: 0.8176 (mttp) cc_final: 0.7919 (mmtm)
REVERT: A  487 ASP cc_start: 0.7493 (t0) cc_final: 0.7194 (t70)
REVERT: B   27 ASP cc_start: 0.8007 (m-30) cc_final: 0.7732 (m-30)
REVERT: B  275 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7227 (mp0)
REVERT: B  368 GLU cc_start: 0.8450 (tt0) cc_final: 0.8239 (pt0)
  outliers start: 26
  outliers final: 22
  residues processed: 186
  average time/residue: 0.2950
  time to fit residues: 76.7929
Evaluate side-chains
  178 residues out of total 1465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 156
  time to evaluate  : 1.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  273 THR
Chi-restraints excluded: chain C residue  291 THR
Chi-restraints excluded: chain C residue  442 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain A residue  490 LYS
Chi-restraints excluded: chain B residue  118 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  335 ILE
Chi-restraints excluded: chain B residue  457 ASP
Chi-restraints excluded: chain B residue  477 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 133 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 119 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   chunk 136 optimal weight:    1.9990
   chunk 110 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 81 optimal weight:    2.9990
   chunk 144 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
** L  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 355 HIS
A 210 ASN
B 191 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.3798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.098  13788  Z= 0.477
  Angle     :  0.674   7.063  18675  Z= 0.355
  Chirality :  0.047   0.264   2062
  Planarity :  0.005   0.055   2399
  Dihedral  :  5.777  58.993   2187
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  :  9.42 %
    Favored  : 87.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.20), residues: 1662
  helix:  1.85 (0.27), residues: 329
  sheet:  0.47 (0.26), residues: 388
  loop : -0.74 (0.19), residues: 945

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H 103 
 HIS   0.010   0.002   HIS B 117 
 PHE   0.050   0.003   PHE A 118 
 TYR   0.019   0.002   TYR L  49 
 ARG   0.004   0.001   ARG L  54 

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

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

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 166
  time to evaluate  : 1.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  100 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8543 (m-80)
REVERT: L   90 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8557 (pp30)
REVERT: L   92 ASN cc_start: 0.8731 (t0) cc_final: 0.8386 (t0)
REVERT: C  112 LEU cc_start: 0.8174 (mt) cc_final: 0.7943 (mt)
REVERT: C  188 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7717 (mt-10)
REVERT: C  432 GLU cc_start: 0.8246 (mm-30) cc_final: 0.8022 (mm-30)
REVERT: C  441 ASP cc_start: 0.8394 (m-30) cc_final: 0.8002 (m-30)
REVERT: C  445 LYS cc_start: 0.8655 (tptp) cc_final: 0.8171 (ttmm)
REVERT: B   27 ASP cc_start: 0.8041 (m-30) cc_final: 0.7767 (m-30)
REVERT: B   59 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8408 (tp)
REVERT: B  190 GLU cc_start: 0.7600 (tt0) cc_final: 0.7279 (tt0)
REVERT: B  276 ASN cc_start: 0.7749 (t0) cc_final: 0.7534 (t0)
REVERT: B  348 ASP cc_start: 0.7147 (t0) cc_final: 0.6943 (t0)
REVERT: B  368 GLU cc_start: 0.8470 (tt0) cc_final: 0.8266 (pt0)
  outliers start: 43
  outliers final: 34
  residues processed: 200
  average time/residue: 0.3020
  time to fit residues: 84.0935
Evaluate side-chains
  189 residues out of total 1465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 153
  time to evaluate  : 1.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain H residue  100 PHE
Chi-restraints excluded: chain H residue  109 VAL
Chi-restraints excluded: chain H residue  110 ILE
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain C residue   63 ASP
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  118 PHE
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  273 THR
Chi-restraints excluded: chain C residue  291 THR
Chi-restraints excluded: chain C residue  369 SER
Chi-restraints excluded: chain C residue  389 ASN
Chi-restraints excluded: chain C residue  442 SER
Chi-restraints excluded: chain A residue  118 PHE
Chi-restraints excluded: chain A residue  137 ARG
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  434 GLU
Chi-restraints excluded: chain A residue  442 SER
Chi-restraints excluded: chain A residue  490 LYS
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  118 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  335 ILE
Chi-restraints excluded: chain B residue  457 ASP
Chi-restraints excluded: chain B residue  477 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 144 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 94 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 160 optimal weight:    2.9990
   chunk 133 optimal weight:    0.9980
   chunk 74 optimal weight:    0.7980
   chunk 13 optimal weight:    9.9990
   chunk 84 optimal weight:    1.9990
   chunk 154 optimal weight:    2.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** L  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 160 ASN
A 210 ASN
B 401 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.3903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  13788  Z= 0.259
  Angle     :  0.532   5.407  18675  Z= 0.285
  Chirality :  0.043   0.244   2062
  Planarity :  0.004   0.041   2399
  Dihedral  :  5.366  46.207   2187
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 11.13 %
    Favored  : 86.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.20), residues: 1662
  helix:  2.13 (0.27), residues: 333
  sheet:  0.56 (0.27), residues: 391
  loop : -0.71 (0.19), residues: 938

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  84 
 HIS   0.008   0.001   HIS B 355 
 PHE   0.027   0.002   PHE A 118 
 TYR   0.011   0.002   TYR A  17 
 ARG   0.005   0.000   ARG C 435 

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

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

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 161
  time to evaluate  : 1.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  100 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8432 (m-80)
REVERT: L   92 ASN cc_start: 0.8629 (t0) cc_final: 0.8386 (t0)
REVERT: C  112 LEU cc_start: 0.8001 (mt) cc_final: 0.7751 (mt)
REVERT: C  188 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7697 (mt-10)
REVERT: C  445 LYS cc_start: 0.8630 (tptp) cc_final: 0.8134 (ttmm)
REVERT: B   27 ASP cc_start: 0.8029 (m-30) cc_final: 0.7747 (m-30)
REVERT: B   59 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8388 (tp)
  outliers start: 28
  outliers final: 25
  residues processed: 183
  average time/residue: 0.3040
  time to fit residues: 78.1723
Evaluate side-chains
  182 residues out of total 1465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 155
  time to evaluate  : 1.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain H residue  100 PHE
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain C residue   46 THR
Chi-restraints excluded: chain C residue   63 ASP
Chi-restraints excluded: chain C residue  118 PHE
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  273 THR
Chi-restraints excluded: chain C residue  291 THR
Chi-restraints excluded: chain C residue  442 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  434 GLU
Chi-restraints excluded: chain A residue  490 LYS
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   93 ARG
Chi-restraints excluded: chain B residue  118 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  277 CYS
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  335 ILE
Chi-restraints excluded: chain B residue  346 MET
Chi-restraints excluded: chain B residue  457 ASP
Chi-restraints excluded: chain B residue  477 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 91 optimal weight:    0.0020
   chunk 117 optimal weight:    6.9990
   chunk 90 optimal weight:    2.9990
   chunk 135 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9990
   chunk 159 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 73 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   overall best weight:    0.6990

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

Flipped N/Q/H residues before XYZ refinement:
** L  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 454 GLN
A 210 ASN
B 483 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.3991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13788  Z= 0.178
  Angle     :  0.493   6.738  18675  Z= 0.265
  Chirality :  0.041   0.221   2062
  Planarity :  0.003   0.037   2399
  Dihedral  :  4.976  47.164   2187
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 11.88 %
    Favored  : 86.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.20), residues: 1662
  helix:  2.39 (0.27), residues: 333
  sheet:  0.66 (0.27), residues: 391
  loop : -0.68 (0.19), residues: 938

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  84 
 HIS   0.003   0.001   HIS B 355 
 PHE   0.026   0.002   PHE A 118 
 TYR   0.018   0.001   TYR L  49 
 ARG   0.004   0.000   ARG C 435 

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

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

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 165
  time to evaluate  : 1.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  100 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8331 (m-80)
REVERT: C  112 LEU cc_start: 0.7938 (mt) cc_final: 0.7660 (mt)
REVERT: C  188 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7687 (mt-10)
REVERT: C  445 LYS cc_start: 0.8597 (tptp) cc_final: 0.8107 (mttp)
REVERT: B   27 ASP cc_start: 0.8030 (m-30) cc_final: 0.7731 (m-30)
  outliers start: 25
  outliers final: 22
  residues processed: 184
  average time/residue: 0.2865
  time to fit residues: 74.2390
Evaluate side-chains
  180 residues out of total 1465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 157
  time to evaluate  : 1.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain H residue  100 PHE
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain C residue   63 ASP
Chi-restraints excluded: chain C residue  118 PHE
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  273 THR
Chi-restraints excluded: chain C residue  291 THR
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  434 GLU
Chi-restraints excluded: chain B residue   93 ARG
Chi-restraints excluded: chain B residue  118 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  335 ILE
Chi-restraints excluded: chain B residue  346 MET
Chi-restraints excluded: chain B residue  457 ASP
Chi-restraints excluded: chain B residue  477 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 95 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 101 optimal weight:    3.9990
   chunk 109 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 14 optimal weight:    9.9990
   chunk 125 optimal weight:    4.9990
   chunk 145 optimal weight:    4.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
** L  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 160 ASN
A 210 ASN
B 483 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.4067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.098  13788  Z= 0.476
  Angle     :  0.640   6.187  18675  Z= 0.336
  Chirality :  0.047   0.250   2062
  Planarity :  0.004   0.043   2399
  Dihedral  :  5.584  55.604   2187
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 11.81 %
    Favored  : 86.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.20), residues: 1662
  helix:  2.01 (0.27), residues: 331
  sheet:  0.41 (0.26), residues: 395
  loop : -0.77 (0.19), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 343 
 HIS   0.008   0.002   HIS B 183 
 PHE   0.047   0.003   PHE A 118 
 TYR   0.015   0.002   TYR L  91 
 ARG   0.004   0.001   ARG C 229 

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

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

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 151
  time to evaluate  : 1.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  100 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8445 (m-80)
REVERT: C  112 LEU cc_start: 0.8100 (mt) cc_final: 0.7859 (mt)
REVERT: C  188 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7714 (mt-10)
REVERT: B   27 ASP cc_start: 0.8043 (m-30) cc_final: 0.7763 (m-30)
  outliers start: 31
  outliers final: 28
  residues processed: 175
  average time/residue: 0.2700
  time to fit residues: 67.9198
Evaluate side-chains
  179 residues out of total 1465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 150
  time to evaluate  : 1.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   77 GLN
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain H residue  100 PHE
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain C residue   46 THR
Chi-restraints excluded: chain C residue   63 ASP
Chi-restraints excluded: chain C residue  118 PHE
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  273 THR
Chi-restraints excluded: chain C residue  277 CYS
Chi-restraints excluded: chain C residue  291 THR
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  389 ASN
Chi-restraints excluded: chain C residue  442 SER
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  490 LYS
Chi-restraints excluded: chain B residue  118 PHE
Chi-restraints excluded: chain B residue  155 THR
Chi-restraints excluded: chain B residue  277 CYS
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  335 ILE
Chi-restraints excluded: chain B residue  346 MET
Chi-restraints excluded: chain B residue  457 ASP
Chi-restraints excluded: chain B residue  477 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 153 optimal weight:    0.9990
   chunk 139 optimal weight:    0.5980
   chunk 149 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 117 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 134 optimal weight:    1.9990
   chunk 141 optimal weight:    0.9980
   chunk 148 optimal weight:    0.0980
   chunk 97 optimal weight:    3.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 210 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.4124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13788  Z= 0.187
  Angle     :  0.496   6.527  18675  Z= 0.267
  Chirality :  0.041   0.236   2062
  Planarity :  0.003   0.034   2399
  Dihedral  :  5.168  57.972   2187
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 12.42 %
    Favored  : 86.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.20), residues: 1662
  helix:  2.34 (0.27), residues: 333
  sheet:  0.63 (0.27), residues: 391
  loop : -0.69 (0.20), residues: 938

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  84 
 HIS   0.003   0.001   HIS B 117 
 PHE   0.022   0.002   PHE A 118 
 TYR   0.009   0.001   TYR H  98 
 ARG   0.004   0.000   ARG C 435 

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

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

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 157
  time to evaluate  : 1.627 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  100 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8282 (m-80)
REVERT: C  112 LEU cc_start: 0.7937 (mt) cc_final: 0.7669 (mt)
REVERT: C  188 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7699 (mt-10)
REVERT: C  490 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8459 (ttmt)
REVERT: A  186 ASN cc_start: 0.7455 (t0) cc_final: 0.7213 (t0)
REVERT: A  401 ASN cc_start: 0.8403 (p0) cc_final: 0.8190 (p0)
REVERT: B   27 ASP cc_start: 0.8101 (m-30) cc_final: 0.7801 (m-30)
  outliers start: 23
  outliers final: 20
  residues processed: 175
  average time/residue: 0.2876
  time to fit residues: 71.3071
Evaluate side-chains
  172 residues out of total 1465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 151
  time to evaluate  : 1.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   77 GLN
Chi-restraints excluded: chain H residue  100 PHE
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain C residue   63 ASP
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  273 THR
Chi-restraints excluded: chain C residue  291 THR
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  442 SER
Chi-restraints excluded: chain C residue  477 CYS
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   93 ARG
Chi-restraints excluded: chain B residue  118 PHE
Chi-restraints excluded: chain B residue  277 CYS
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  335 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 157 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 109 optimal weight:    2.9990
   chunk 165 optimal weight:    0.0170
   chunk 152 optimal weight:    3.9990
   chunk 131 optimal weight:    8.9990
   chunk 13 optimal weight:    0.7980
   chunk 101 optimal weight:    3.9990
   chunk 80 optimal weight:    0.6980
   chunk 104 optimal weight:    4.9990
   overall best weight:    1.0820

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

Flipped N/Q/H residues before XYZ refinement:
A 210 ASN
B 401 ASN
B 483 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.4145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  13788  Z= 0.231
  Angle     :  0.514   5.571  18675  Z= 0.274
  Chirality :  0.042   0.225   2062
  Planarity :  0.004   0.036   2399
  Dihedral  :  5.159  59.914   2187
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 12.63 %
    Favored  : 85.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.20), residues: 1662
  helix:  2.41 (0.27), residues: 333
  sheet:  0.53 (0.27), residues: 405
  loop : -0.67 (0.20), residues: 924

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  84 
 HIS   0.004   0.001   HIS A 130 
 PHE   0.028   0.002   PHE A 118 
 TYR   0.020   0.001   TYR L  49 
 ARG   0.004   0.000   ARG C 435 

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

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

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3324 Ramachandran restraints generated.
    1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 156
  time to evaluate  : 1.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  100 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.8300 (m-80)
REVERT: C  112 LEU cc_start: 0.7947 (mt) cc_final: 0.7668 (mt)
REVERT: C  188 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7701 (mt-10)
REVERT: C  445 LYS cc_start: 0.8610 (tptp) cc_final: 0.8106 (mttp)
REVERT: A  186 ASN cc_start: 0.7475 (t0) cc_final: 0.7224 (t0)
REVERT: A  401 ASN cc_start: 0.8430 (p0) cc_final: 0.8205 (p0)
REVERT: B   27 ASP cc_start: 0.8097 (m-30) cc_final: 0.7816 (m-30)
  outliers start: 24
  outliers final: 21
  residues processed: 175
  average time/residue: 0.2939
  time to fit residues: 72.0260
Evaluate side-chains
  174 residues out of total 1465 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 152
  time to evaluate  : 1.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   77 GLN
Chi-restraints excluded: chain H residue  100 PHE
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   85 VAL
Chi-restraints excluded: chain C residue   63 ASP
Chi-restraints excluded: chain C residue  118 PHE
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  273 THR
Chi-restraints excluded: chain C residue  291 THR
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  442 SER
Chi-restraints excluded: chain C residue  477 CYS
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   93 ARG
Chi-restraints excluded: chain B residue  118 PHE
Chi-restraints excluded: chain B residue  277 CYS
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  335 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 140 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 121 optimal weight:    0.7980
   chunk 19 optimal weight:    7.9990
   chunk 36 optimal weight:    0.6980
   chunk 131 optimal weight:    6.9990
   chunk 55 optimal weight:    5.9990
   chunk 135 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 115 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 210 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.119488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.099172 restraints weight = 18562.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 1.77
r_work: 0.3046 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2913 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.4201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13788  Z= 0.190
  Angle     :  0.486   5.681  18675  Z= 0.261
  Chirality :  0.041   0.212   2062
  Planarity :  0.003   0.034   2399
  Dihedral  :  4.952  55.565   2187
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 12.42 %
    Favored  : 85.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.21), residues: 1662
  helix:  2.52 (0.27), residues: 333
  sheet:  0.59 (0.27), residues: 405
  loop : -0.64 (0.20), residues: 924

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  84 
 HIS   0.003   0.001   HIS A 295 
 PHE   0.023   0.002   PHE C 118 
 TYR   0.009   0.001   TYR A  17 
 ARG   0.004   0.000   ARG C 435 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2941.57 seconds
wall clock time: 53 minutes 46.71 seconds (3226.71 seconds total)