Starting phenix.real_space_refine
on Wed Dec 13 12:17:56 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/12_2023/6zb4_11144_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/12_2023/6zb4_11144.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/12_2023/6zb4_11144.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/12_2023/6zb4_11144.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/12_2023/6zb4_11144_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb4_11144/12_2023/6zb4_11144_updated.pdb"
  }
  resolution = 3.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.010
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     114      5.16       5
     C   15856      2.51       5
     N    4094      2.21       5
     O    4777      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "C TYR   37": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG   78": "NH1" <-> "NH2"
    Residue "C PHE   86": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   92": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  111": "OD1" <-> "OD2"
    Residue "C PHE  168": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  169": "OE1" <-> "OE2"
    Residue "C ARG  237": "NH1" <-> "NH2"
    Residue "C GLU  298": "OE1" <-> "OE2"
    Residue "C TYR  313": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  324": "OE1" <-> "OE2"
    Residue "C TYR  351": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  365": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  380": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  423": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  427": "OD1" <-> "OD2"
    Residue "C GLU  465": "OE1" <-> "OE2"
    Residue "C GLU  484": "OE1" <-> "OE2"
    Residue "C TYR  505": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  562": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  568": "OD1" <-> "OD2"
    Residue "C GLU  583": "OE1" <-> "OE2"
    Residue "C ARG  646": "NH1" <-> "NH2"
    Residue "C TYR  692": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  745": "OE1" <-> "OE2"
    Residue "C GLU  865": "OE1" <-> "OE2"
    Residue "C ASP  947": "OD1" <-> "OD2"
    Residue "C GLU 1028": "OE1" <-> "OE2"
    Residue "C PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU 1089": "OE1" <-> "OE2"
    Residue "B PHE   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE   43": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG   78": "NH1" <-> "NH2"
    Residue "B PHE  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  168": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  169": "OE1" <-> "OE2"
    Residue "B GLU  191": "OE1" <-> "OE2"
    Residue "B ARG  237": "NH1" <-> "NH2"
    Residue "B ASP  290": "OD1" <-> "OD2"
    Residue "B GLU  298": "OE1" <-> "OE2"
    Residue "B GLU  309": "OE1" <-> "OE2"
    Residue "B TYR  313": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  342": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  392": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  423": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  427": "OD1" <-> "OD2"
    Residue "B ASP  428": "OD1" <-> "OD2"
    Residue "B GLU  516": "OE1" <-> "OE2"
    Residue "B PHE  562": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  583": "OE1" <-> "OE2"
    Residue "B ASP  586": "OD1" <-> "OD2"
    Residue "B TYR  612": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  646": "NH1" <-> "NH2"
    Residue "B GLU  699": "OE1" <-> "OE2"
    Residue "B TYR  704": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  715": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  756": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  777": "OE1" <-> "OE2"
    Residue "B ARG  844": "NH1" <-> "NH2"
    Residue "B GLU  865": "OE1" <-> "OE2"
    Residue "B GLU  915": "OE1" <-> "OE2"
    Residue "B ASP  947": "OD1" <-> "OD2"
    Residue "B GLU 1028": "OE1" <-> "OE2"
    Residue "B GLU 1069": "OE1" <-> "OE2"
    Residue "B PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP 1124": "OD1" <-> "OD2"
    Residue "A TYR   28": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   65": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG   78": "NH1" <-> "NH2"
    Residue "A ARG  158": "NH1" <-> "NH2"
    Residue "A ARG  237": "NH1" <-> "NH2"
    Residue "A GLU  281": "OE1" <-> "OE2"
    Residue "A GLU  298": "OE1" <-> "OE2"
    Residue "A GLU  324": "OE1" <-> "OE2"
    Residue "A PHE  377": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  427": "OD1" <-> "OD2"
    Residue "A GLU  471": "OE1" <-> "OE2"
    Residue "A GLU  484": "OE1" <-> "OE2"
    Residue "A GLU  516": "OE1" <-> "OE2"
    Residue "A GLU  583": "OE1" <-> "OE2"
    Residue "A ARG  646": "NH1" <-> "NH2"
    Residue "A GLU  661": "OE1" <-> "OE2"
    Residue "A GLU  745": "OE1" <-> "OE2"
    Residue "A PHE  756": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  933": "OD1" <-> "OD2"
    Residue "A ASP  976": "OD1" <-> "OD2"
    Residue "A GLU 1028": "OE1" <-> "OE2"
    Residue "A ASP 1081": "OD1" <-> "OD2"
    Residue "A GLU 1089": "OE1" <-> "OE2"
    Residue "A GLU 1108": "OE1" <-> "OE2"
    Residue "A ASP 1115": "OD1" <-> "OD2"
  Time to flip residues: 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 24841
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "C"
      Number of atoms: 8056
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1035, 8056
          Classifications: {'peptide': 1035}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 47, 'TRANS': 987}
          Chain breaks: 11
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "B"
      Number of atoms: 8189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1050, 8189
          Classifications: {'peptide': 1050}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 47, 'TRANS': 1002}
          Chain breaks: 10
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 8158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1048, 8158
          Classifications: {'peptide': 1048}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 48, 'TRANS': 999}
          Chain breaks: 11
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 104
          Unusual residues: {'EIC': 1, 'NAG': 6}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "B"
      Number of atoms: 160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 160
          Unusual residues: {'EIC': 1, 'NAG': 10}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 10
    Chain: "A"
      Number of atoms: 146
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 146
          Unusual residues: {'EIC': 1, 'NAG': 9}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 9
  Time building chain proxies: 13.12, per 1000 atoms: 0.53
  Number of scatterers: 24841
  At special positions: 0
  Unit cell: (143.85, 151.2, 161.7, 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     114     16.00
     O    4777      8.00
     N    4094      7.00
     C   15856      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=31, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 291 " - pdb=" SG  CYS C 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 538 " - pdb=" SG  CYS C 590 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 617 " - pdb=" SG  CYS C 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 662 " - pdb=" SG  CYS C 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 740 " - pdb=" SG  CYS C 746 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 837 " - pdb=" SG  CYS C 848 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1029 " - pdb=" SG  CYS C1040 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 538 " - pdb=" SG  CYS B 590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 617 " - pdb=" SG  CYS B 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 662 " - pdb=" SG  CYS B 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 740 " - pdb=" SG  CYS B 746 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 837 " - pdb=" SG  CYS B 848 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1029 " - pdb=" SG  CYS B1040 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 617 " - pdb=" SG  CYS A 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 662 " - pdb=" SG  CYS A 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 740 " - pdb=" SG  CYS A 746 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 837 " - pdb=" SG  CYS A 848 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1029 " - pdb=" SG  CYS A1040 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Atom "HETATM24659  O5  NAG B1309 .*.     O  " rejected from bonding due to valence issues.
  Atom "HETATM24443  O5  NAG C1401 .*.     O  " rejected from bonding due to valence issues.
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG A2102 " - " ASN A 714 "
      " NAG A2104 " - " ASN A 343 "
      " NAG B1309 " - " ASN B 234 "
      " NAG C1403 " - " ASN C 616 "
      " NAG C1406 " - " ASN C 234 "
      " NAG D   1 " - " ASN C 714 "
  Time building additional restraints: 8.38
  Conformation dependent library (CDL) restraints added in 4.2 seconds
  

  6126 Ramachandran restraints generated.
    3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5852

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      57 helices and 41 sheets defined
      20.1% alpha, 17.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 6.27
  Creating SS restraints...
    Processing helix  chain 'C' and resid 295 through 303
    Processing helix  chain 'C' and resid 338 through 342
    Processing helix  chain 'C' and resid 350 through 352
      No H-bonds generated for 'chain 'C' and resid 350 through 352'
    Processing helix  chain 'C' and resid 365 through 370
      removed outlier: 3.602A  pdb=" N   TYR C 369 " --> pdb=" O   SER C 366 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ASN C 370 " --> pdb=" O   VAL C 367 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 384 through 386
      No H-bonds generated for 'chain 'C' and resid 384 through 386'
    Processing helix  chain 'C' and resid 404 through 409
      removed outlier: 3.654A  pdb=" N   VAL C 407 " --> pdb=" O   GLY C 404 " (cutoff:3.500A)
      removed outlier: 5.031A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 417 through 420
      No H-bonds generated for 'chain 'C' and resid 417 through 420'
    Processing helix  chain 'C' and resid 735 through 739
    Processing helix  chain 'C' and resid 745 through 752
      removed outlier: 4.104A  pdb=" N   GLN C 752 " --> pdb=" O   ASN C 748 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 756 through 779
      removed outlier: 3.599A  pdb=" N   LEU C 760 " --> pdb=" O   PHE C 756 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ASP C 772 " --> pdb=" O   ALA C 768 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LYS C 773 " --> pdb=" O   VAL C 769 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   THR C 775 " --> pdb=" O   GLN C 771 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 814 through 820
    Processing helix  chain 'C' and resid 834 through 837
      No H-bonds generated for 'chain 'C' and resid 834 through 837'
    Processing helix  chain 'C' and resid 864 through 886
      removed outlier: 8.270A  pdb=" N   TRP C 883 " --> pdb=" O   ILE C 879 " (cutoff:3.500A)
      removed outlier: 8.168A  pdb=" N   THR C 884 " --> pdb=" O   THR C 880 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   PHE C 885 " --> pdb=" O   SER C 881 " (cutoff:3.500A)
      removed outlier: 5.769A  pdb=" N   GLY C 886 " --> pdb=" O   GLY C 882 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 895 through 906
      removed outlier: 3.693A  pdb=" N   ALA C 900 " --> pdb=" O   ALA C 896 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   TYR C 901 " --> pdb=" O   MET C 897 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE C 906 " --> pdb=" O   ARG C 902 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 911 through 915
    Processing helix  chain 'C' and resid 917 through 935
    Processing helix  chain 'C' and resid 943 through 964
      removed outlier: 3.942A  pdb=" N   VAL C 948 " --> pdb=" O   LYS C 944 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL C 949 " --> pdb=" O   LEU C 945 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LEU C 956 " --> pdb=" O   ASN C 952 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   LEU C 963 " --> pdb=" O   LEU C 959 " (cutoff:3.500A)
      removed outlier: 5.055A  pdb=" N   SER C 964 " --> pdb=" O   VAL C 960 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 974 through 977
      No H-bonds generated for 'chain 'C' and resid 974 through 977'
    Processing helix  chain 'C' and resid 987 through 1028
      removed outlier: 3.838A  pdb=" N   ARG C 992 " --> pdb=" O   VAL C 988 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ALA C1013 " --> pdb=" O   LEU C1009 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   GLU C1014 " --> pdb=" O   ILE C1010 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ILE C1015 " --> pdb=" O   ARG C1011 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   SER C1027 " --> pdb=" O   ALA C1023 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 302
    Processing helix  chain 'B' and resid 339 through 342
      No H-bonds generated for 'chain 'B' and resid 339 through 342'
    Processing helix  chain 'B' and resid 350 through 352
      No H-bonds generated for 'chain 'B' and resid 350 through 352'
    Processing helix  chain 'B' and resid 365 through 367
      No H-bonds generated for 'chain 'B' and resid 365 through 367'
    Processing helix  chain 'B' and resid 384 through 386
      No H-bonds generated for 'chain 'B' and resid 384 through 386'
    Processing helix  chain 'B' and resid 404 through 409
      removed outlier: 4.967A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 421
      removed outlier: 3.673A  pdb=" N   TYR B 421 " --> pdb=" O   LYS B 417 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 417 through 421'
    Processing helix  chain 'B' and resid 735 through 739
    Processing helix  chain 'B' and resid 744 through 752
      removed outlier: 3.910A  pdb=" N   LEU B 751 " --> pdb=" O   SER B 747 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   GLN B 752 " --> pdb=" O   ASN B 748 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 756 through 779
      removed outlier: 3.850A  pdb=" N   ASP B 772 " --> pdb=" O   ALA B 768 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LYS B 773 " --> pdb=" O   VAL B 769 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   THR B 775 " --> pdb=" O   GLN B 771 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   VAL B 778 " --> pdb=" O   ASN B 774 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 814 through 820
    Processing helix  chain 'B' and resid 848 through 853
      removed outlier: 3.975A  pdb=" N   ASN B 853 " --> pdb=" O   ALA B 849 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 864 through 881
    Processing helix  chain 'B' and resid 884 through 886
      No H-bonds generated for 'chain 'B' and resid 884 through 886'
    Processing helix  chain 'B' and resid 895 through 904
      removed outlier: 3.756A  pdb=" N   TYR B 901 " --> pdb=" O   MET B 897 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 911 through 914
      No H-bonds generated for 'chain 'B' and resid 911 through 914'
    Processing helix  chain 'B' and resid 917 through 935
    Processing helix  chain 'B' and resid 943 through 964
      removed outlier: 4.439A  pdb=" N   VAL B 948 " --> pdb=" O   LYS B 944 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   VAL B 949 " --> pdb=" O   LEU B 945 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   LEU B 956 " --> pdb=" O   ASN B 952 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   LEU B 963 " --> pdb=" O   LEU B 959 " (cutoff:3.500A)
      removed outlier: 4.934A  pdb=" N   SER B 964 " --> pdb=" O   VAL B 960 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 974 through 980
      removed outlier: 3.628A  pdb=" N   ARG B 980 " --> pdb=" O   ASP B 976 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 983 through 1028
      removed outlier: 3.987A  pdb=" N   GLU B 987 " --> pdb=" O   LYS B 983 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   VAL B 988 " --> pdb=" O   VAL B 984 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   GLN B 989 " --> pdb=" O   GLU B 985 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ARG B 992 " --> pdb=" O   VAL B 988 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU B 993 " --> pdb=" O   GLN B 989 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ALA B1013 " --> pdb=" O   LEU B1009 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   GLU B1014 " --> pdb=" O   ILE B1010 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   SER B1027 " --> pdb=" O   ALA B1023 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 303
    Processing helix  chain 'A' and resid 338 through 342
    Processing helix  chain 'A' and resid 365 through 369
    Processing helix  chain 'A' and resid 384 through 386
      No H-bonds generated for 'chain 'A' and resid 384 through 386'
    Processing helix  chain 'A' and resid 404 through 409
      removed outlier: 4.906A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 420
      No H-bonds generated for 'chain 'A' and resid 417 through 420'
    Processing helix  chain 'A' and resid 735 through 739
    Processing helix  chain 'A' and resid 745 through 752
      removed outlier: 4.552A  pdb=" N   GLN A 752 " --> pdb=" O   ASN A 748 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 757 through 779
      removed outlier: 3.772A  pdb=" N   ALA A 763 " --> pdb=" O   GLN A 759 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ASP A 772 " --> pdb=" O   ALA A 768 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LYS A 773 " --> pdb=" O   VAL A 769 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   THR A 775 " --> pdb=" O   GLN A 771 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL A 778 " --> pdb=" O   ASN A 774 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 814 through 821
    Processing helix  chain 'A' and resid 834 through 837
      No H-bonds generated for 'chain 'A' and resid 834 through 837'
    Processing helix  chain 'A' and resid 864 through 880
    Processing helix  chain 'A' and resid 895 through 906
      removed outlier: 3.771A  pdb=" N   TYR A 901 " --> pdb=" O   MET A 897 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   ILE A 906 " --> pdb=" O   ARG A 902 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 911 through 914
      No H-bonds generated for 'chain 'A' and resid 911 through 914'
    Processing helix  chain 'A' and resid 917 through 936
    Processing helix  chain 'A' and resid 943 through 963
      removed outlier: 4.302A  pdb=" N   VAL A 948 " --> pdb=" O   LYS A 944 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   VAL A 949 " --> pdb=" O   LEU A 945 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LEU A 956 " --> pdb=" O   ASN A 952 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   LEU A 963 " --> pdb=" O   LEU A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 980
    Processing helix  chain 'A' and resid 983 through 1029
      removed outlier: 3.706A  pdb=" N   VAL A 988 " --> pdb=" O   VAL A 984 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLN A 989 " --> pdb=" O   GLU A 985 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ARG A 992 " --> pdb=" O   VAL A 988 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU A 993 " --> pdb=" O   GLN A 989 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ALA A1013 " --> pdb=" O   LEU A1009 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLU A1014 " --> pdb=" O   ILE A1010 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'C' and resid 28 through 31
      removed outlier: 3.536A  pdb=" N   THR C  63 " --> pdb=" O   VAL C 267 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   VAL C 267 " --> pdb=" O   THR C  63 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ILE C 203 " --> pdb=" O   VAL C 227 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   VAL C 227 " --> pdb=" O   ILE C 203 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   SER C 205 " --> pdb=" O   PRO C 225 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'C' and resid 48 through 55
      removed outlier: 4.072A  pdb=" N   ASP C 287 " --> pdb=" O   LYS C 278 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'C' and resid 83 through 85
    Processing sheet with id=  D, first strand: chain 'C' and resid 311 through 314
    Processing sheet with id=  E, first strand: chain 'C' and resid 325 through 328
      removed outlier: 6.293A  pdb=" N   ASN C 540 " --> pdb=" O   ILE C 326 " (cutoff:3.500A)
      removed outlier: 8.035A  pdb=" N   ARG C 328 " --> pdb=" O   ASN C 540 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   ASN C 542 " --> pdb=" O   ARG C 328 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'C' and resid 354 through 358
      removed outlier: 4.245A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   THR C 376 " --> pdb=" O   ALA C 435 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=  H, first strand: chain 'C' and resid 584 through 586
      removed outlier: 6.475A  pdb=" N   GLY C 566 " --> pdb=" O   ASP C 574 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'C' and resid 689 through 693
      removed outlier: 6.384A  pdb=" N   ALA C 672 " --> pdb=" O   PRO C 665 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'C' and resid 708 through 710
    Processing sheet with id=  K, first strand: chain 'C' and resid 731 through 733
    Processing sheet with id=  L, first strand: chain 'C' and resid 1091 through 1094
    Processing sheet with id=  M, first strand: chain 'C' and resid 714 through 725
      removed outlier: 3.968A  pdb=" N   ASN C 714 " --> pdb=" O   GLN C1068 " (cutoff:3.500A)
      removed outlier: 5.560A  pdb=" N   THR C 716 " --> pdb=" O   PRO C1066 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   SER C 718 " --> pdb=" O   TYR C1064 " (cutoff:3.500A)
      removed outlier: 5.460A  pdb=" N   TYR C1064 " --> pdb=" O   SER C 718 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   THR C 720 " --> pdb=" O   VAL C1062 " (cutoff:3.500A)
      removed outlier: 5.667A  pdb=" N   VAL C1062 " --> pdb=" O   THR C 720 " (cutoff:3.500A)
      removed outlier: 7.599A  pdb=" N   GLU C 722 " --> pdb=" O   LEU C1060 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   LEU C1060 " --> pdb=" O   GLU C 722 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   LEU C 724 " --> pdb=" O   VAL C1058 " (cutoff:3.500A)
      removed outlier: 5.521A  pdb=" N   VAL C1058 " --> pdb=" O   LEU C 724 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ALA C1053 " --> pdb=" O   GLY C1056 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   TYR C1064 " --> pdb=" O   HIS C1045 " (cutoff:3.500A)
      removed outlier: 5.864A  pdb=" N   HIS C1045 " --> pdb=" O   TYR C1064 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'B' and resid 27 through 29
      removed outlier: 3.751A  pdb=" N   ALA B  27 " --> pdb=" O   TRP B  64 " (cutoff:3.500A)
    Processing sheet with id=  O, first strand: chain 'B' and resid 48 through 55
      removed outlier: 3.541A  pdb=" N   LYS B 278 " --> pdb=" O   ASP B 287 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   ASP B 287 " --> pdb=" O   LYS B 278 " (cutoff:3.500A)
    Processing sheet with id=  P, first strand: chain 'B' and resid 265 through 269
      removed outlier: 3.771A  pdb=" N   VAL B 227 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   SER B 205 " --> pdb=" O   PRO B 225 " (cutoff:3.500A)
    Processing sheet with id=  Q, first strand: chain 'B' and resid 127 through 131
      removed outlier: 6.682A  pdb=" N   LEU B 241 " --> pdb=" O   ARG B 102 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   TRP B 104 " --> pdb=" O   GLN B 239 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   GLN B 239 " --> pdb=" O   TRP B 104 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   PHE B 106 " --> pdb=" O   ARG B 237 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ARG B 237 " --> pdb=" O   PHE B 106 " (cutoff:3.500A)
    Processing sheet with id=  R, first strand: chain 'B' and resid 311 through 314
    Processing sheet with id=  S, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.707A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   SER B 399 " --> pdb=" O   ASN B 354 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
    Processing sheet with id=  T, first strand: chain 'B' and resid 376 through 379
      removed outlier: 3.542A  pdb=" N   THR B 376 " --> pdb=" O   ALA B 435 " (cutoff:3.500A)
    Processing sheet with id=  U, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=  V, first strand: chain 'B' and resid 539 through 543
    Processing sheet with id=  W, first strand: chain 'B' and resid 551 through 554
    Processing sheet with id=  X, first strand: chain 'B' and resid 688 through 693
      removed outlier: 6.276A  pdb=" N   ALA B 672 " --> pdb=" O   PRO B 665 " (cutoff:3.500A)
    Processing sheet with id=  Y, first strand: chain 'B' and resid 715 through 725
      removed outlier: 3.577A  pdb=" N   SER B 718 " --> pdb=" O   THR B1063 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   TYR B1064 " --> pdb=" O   HIS B1045 " (cutoff:3.500A)
      removed outlier: 5.842A  pdb=" N   HIS B1045 " --> pdb=" O   TYR B1064 " (cutoff:3.500A)
    Processing sheet with id=  Z, first strand: chain 'B' and resid 731 through 733
    Processing sheet with id= AA, first strand: chain 'B' and resid 1091 through 1093
    Processing sheet with id= AB, first strand: chain 'A' and resid 29 through 31
    Processing sheet with id= AC, first strand: chain 'A' and resid 48 through 55
    Processing sheet with id= AD, first strand: chain 'A' and resid 264 through 267
      removed outlier: 5.957A  pdb=" N   SER A 205 " --> pdb=" O   PRO A 225 " (cutoff:3.500A)
    Processing sheet with id= AE, first strand: chain 'A' and resid 127 through 131
      removed outlier: 6.821A  pdb=" N   LEU A 241 " --> pdb=" O   ARG A 102 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   TRP A 104 " --> pdb=" O   GLN A 239 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   GLN A 239 " --> pdb=" O   TRP A 104 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   PHE A 106 " --> pdb=" O   ARG A 237 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ARG A 237 " --> pdb=" O   PHE A 106 " (cutoff:3.500A)
    Processing sheet with id= AF, first strand: chain 'A' and resid 141 through 143
    Processing sheet with id= AG, first strand: chain 'A' and resid 311 through 314
    Processing sheet with id= AH, first strand: chain 'A' and resid 324 through 328
      removed outlier: 4.318A  pdb=" N   GLU A 324 " --> pdb=" O   CYS A 538 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   THR A 553 " --> pdb=" O   ASP A 586 " (cutoff:3.500A)
    Processing sheet with id= AI, first strand: chain 'A' and resid 354 through 358
      removed outlier: 4.571A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
    Processing sheet with id= AJ, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id= AK, first strand: chain 'A' and resid 688 through 693
      removed outlier: 3.573A  pdb=" N   SER A 688 " --> pdb=" O   GLN A 675 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLY A 667 " --> pdb=" O   ILE A 670 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   ALA A 672 " --> pdb=" O   PRO A 665 " (cutoff:3.500A)
    Processing sheet with id= AL, first strand: chain 'A' and resid 708 through 712
    Processing sheet with id= AM, first strand: chain 'A' and resid 715 through 725
      removed outlier: 3.625A  pdb=" N   MET A1047 " --> pdb=" O   VAL A1062 " (cutoff:3.500A)
      removed outlier: 5.622A  pdb=" N   TYR A1064 " --> pdb=" O   HIS A1045 " (cutoff:3.500A)
      removed outlier: 5.637A  pdb=" N   HIS A1045 " --> pdb=" O   TYR A1064 " (cutoff:3.500A)
    Processing sheet with id= AN, first strand: chain 'A' and resid 731 through 733
    Processing sheet with id= AO, first strand: chain 'A' and resid 1091 through 1094

    702 hydrogen bonds defined for protein.
    1926 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: 9.26

  Time building geometry restraints manager: 9.23 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 4043
        1.31 -     1.44: 7056
        1.44 -     1.57: 14142
        1.57 -     1.70: 0
        1.70 -     1.82: 138
  Bond restraints: 25379
  Sorted by residual:
  bond pdb=" C7  NAG B1306 "
       pdb=" N2  NAG B1306 "
    ideal  model  delta    sigma   weight residual
    1.346  1.472 -0.126 2.00e-02 2.50e+03 3.99e+01
  bond pdb=" C7  NAG B1302 "
       pdb=" N2  NAG B1302 "
    ideal  model  delta    sigma   weight residual
    1.346  1.471 -0.125 2.00e-02 2.50e+03 3.90e+01
  bond pdb=" C7  NAG B1307 "
       pdb=" N2  NAG B1307 "
    ideal  model  delta    sigma   weight residual
    1.346  1.471 -0.125 2.00e-02 2.50e+03 3.90e+01
  bond pdb=" C7  NAG B1303 "
       pdb=" N2  NAG B1303 "
    ideal  model  delta    sigma   weight residual
    1.346  1.471 -0.125 2.00e-02 2.50e+03 3.89e+01
  bond pdb=" C7  NAG C1401 "
       pdb=" N2  NAG C1401 "
    ideal  model  delta    sigma   weight residual
    1.346  1.471 -0.125 2.00e-02 2.50e+03 3.89e+01
  ... (remaining 25374 not shown)

  Histogram of bond angle deviations from ideal:
       99.50 -   106.40: 589
      106.40 -   113.31: 13769
      113.31 -   120.21: 8776
      120.21 -   127.12: 11139
      127.12 -   134.02: 210
  Bond angle restraints: 34483
  Sorted by residual:
  angle pdb=" N   ILE B 847 "
        pdb=" CA  ILE B 847 "
        pdb=" C   ILE B 847 "
      ideal   model   delta    sigma   weight residual
     112.96  108.66    4.30 1.00e+00 1.00e+00 1.85e+01
  angle pdb=" N   MET C1047 "
        pdb=" CA  MET C1047 "
        pdb=" C   MET C1047 "
      ideal   model   delta    sigma   weight residual
     107.73  113.36   -5.63 1.34e+00 5.57e-01 1.76e+01
  angle pdb=" N   ALA C 703 "
        pdb=" CA  ALA C 703 "
        pdb=" C   ALA C 703 "
      ideal   model   delta    sigma   weight residual
     110.97  115.07   -4.10 1.09e+00 8.42e-01 1.41e+01
  angle pdb=" CA  TYR B  37 "
        pdb=" CB  TYR B  37 "
        pdb=" CG  TYR B  37 "
      ideal   model   delta    sigma   weight residual
     113.90  120.42   -6.52 1.80e+00 3.09e-01 1.31e+01
  angle pdb=" N   GLY C 697 "
        pdb=" CA  GLY C 697 "
        pdb=" C   GLY C 697 "
      ideal   model   delta    sigma   weight residual
     113.18  121.77   -8.59 2.37e+00 1.78e-01 1.31e+01
  ... (remaining 34478 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.79: 14507
       26.79 -    53.58: 758
       53.58 -    80.38: 114
       80.38 -   107.17: 16
      107.17 -   133.96: 2
  Dihedral angle restraints: 15397
    sinusoidal: 6309
      harmonic: 9088
  Sorted by residual:
  dihedral pdb=" CA  ARG C1088 "
           pdb=" C   ARG C1088 "
           pdb=" N   GLU C1089 "
           pdb=" CA  GLU C1089 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.12   25.88     0      5.00e+00 4.00e-02 2.68e+01
  dihedral pdb=" CA  ASP A  88 "
           pdb=" C   ASP A  88 "
           pdb=" N   GLY A  89 "
           pdb=" CA  GLY A  89 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.79  -24.21     0      5.00e+00 4.00e-02 2.35e+01
  dihedral pdb=" CA  TYR A 753 "
           pdb=" C   TYR A 753 "
           pdb=" N   GLY A 754 "
           pdb=" CA  GLY A 754 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.94   24.06     0      5.00e+00 4.00e-02 2.31e+01
  ... (remaining 15394 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.258: 3970
       0.258 -    0.516: 2
       0.516 -    0.773: 1
       0.773 -    1.031: 0
       1.031 -    1.289: 1
  Chirality restraints: 3974
  Sorted by residual:
  chirality pdb=" C1  NAG B1309 "
            pdb=" ND2 ASN B 234 "
            pdb=" C2  NAG B1309 "
            pdb=" O5  NAG B1309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.11   -1.29 2.00e-01 2.50e+01 4.15e+01
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN C 714 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.85   -0.55 2.00e-01 2.50e+01 7.68e+00
  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   -2.35   -0.05 2.00e-02 2.50e+03 5.15e+00
  ... (remaining 3971 not shown)

  Planarity restraints: 4425
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 234 "    0.495 2.00e-02 2.50e+03   5.08e-01 3.23e+03
        pdb=" CG  ASN B 234 "   -0.178 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 234 "   -0.126 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 234 "   -0.796 2.00e-02 2.50e+03
        pdb=" C1  NAG B1309 "    0.605 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C1402 "    0.303 2.00e-02 2.50e+03   2.54e-01 8.09e+02
        pdb=" C7  NAG C1402 "   -0.080 2.00e-02 2.50e+03
        pdb=" C8  NAG C1402 "    0.189 2.00e-02 2.50e+03
        pdb=" N2  NAG C1402 "   -0.435 2.00e-02 2.50e+03
        pdb=" O7  NAG C1402 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B1304 "   -0.299 2.00e-02 2.50e+03   2.52e-01 7.95e+02
        pdb=" C7  NAG B1304 "    0.077 2.00e-02 2.50e+03
        pdb=" C8  NAG B1304 "   -0.185 2.00e-02 2.50e+03
        pdb=" N2  NAG B1304 "    0.433 2.00e-02 2.50e+03
        pdb=" O7  NAG B1304 "   -0.026 2.00e-02 2.50e+03
  ... (remaining 4422 not shown)

  Histogram of nonbonded interaction distances:
        1.81 -     2.43: 88
        2.43 -     3.05: 15308
        3.05 -     3.67: 32104
        3.67 -     4.28: 51766
        4.28 -     4.90: 91011
  Nonbonded interactions: 190277
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 339 "
            pdb=" OD1 ASN A 343 "
     model   vdw
     1.814 3.040
  nonbonded pdb=" O   ASN C 975 "
            pdb=" OG  SER C 979 "
     model   vdw
     1.949 2.440
  nonbonded pdb=" ND2 ASN C 343 "
            pdb=" O5  NAG C1401 "
     model   vdw
     1.966 2.520
  nonbonded pdb=" O3  NAG B1310 "
            pdb=" O7  NAG B1310 "
     model   vdw
     2.051 2.440
  nonbonded pdb=" O   ASN A 975 "
            pdb=" OG  SER A 979 "
     model   vdw
     2.072 2.440
  ... (remaining 190272 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 15 through 67 or resid 81 through 96 or (resid 97 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 98 through 142 or (res \ 
id 143 and (name N or name CA or name C or name O or name CB )) or resid 157 thr \ 
ough 172 or (resid 187 and (name N or name CA or name C or name O or name CB ))  \ 
or resid 188 through 210 or resid 216 through 245 or resid 255 or resid 257 thro \ 
ugh 675 or resid 686 through 808 or resid 810 through 825 or resid 829 through 8 \ 
40 or resid 845 through 931 or (resid 932 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 933 through 1136 or resid 2101 through 2106))
  selection = (chain 'B' and (resid 15 through 67 or resid 81 through 96 or (resid 97 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 98 through 172 or (res \ 
id 187 and (name N or name CA or name C or name O or name CB )) or resid 188 thr \ 
ough 210 or resid 216 through 255 or resid 257 through 675 or resid 686 through  \ 
807 or (resid 808 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 810 through 840 or resid 845 through 931 or (resid 932 and (name N or name C \ 
A or name C or name O or name CB )) or resid 933 through 936 or (resid 937 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 941 through 1136 or \ 
 resid 1301 through 1306))
  selection = (chain 'C' and (resid 15 through 18 or resid 25 through 67 or resid 81 through 1 \ 
42 or (resid 143 and (name N or name CA or name C or name O or name CB )) or res \ 
id 157 through 245 or resid 256 through 808 or resid 810 through 936 or (resid 9 \ 
37 through 941 and (name N or name CA or name C or name O or name CB )) or resid \ 
 942 through 1136 or resid 1401 through 1406))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          3.720
  Check model and map are aligned:         0.330
  Set scattering table:                    0.180
  Process input model:                     63.070
  Find NCS groups from input model:        1.880
  Set up NCS constraints:                  0.100
  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:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   73.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.126  25379  Z= 0.415
  Angle     :  0.691   8.586  34483  Z= 0.366
  Chirality :  0.051   1.289   3974
  Planarity :  0.009   0.254   4419
  Dihedral  : 16.161 133.959   9452
  Min Nonbonded Distance : 1.814

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  8.19 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 16.85 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.11 (0.12), residues: 3063
  helix: -1.95 (0.17), residues: 659
  sheet: -1.71 (0.18), residues: 689
  loop : -3.65 (0.11), residues: 1715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP A 353 
   HIS   0.003   0.001   HIS B1061 
   PHE   0.014   0.001   PHE C 592 
   TYR   0.020   0.001   TYR A  37 
   ARG   0.003   0.000   ARG A 567 

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

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

  6126 Ramachandran restraints generated.
    3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6126 Ramachandran restraints generated.
    3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  421 residues out of total 2722 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 104
    poor density    : 317
  time to evaluate  : 2.816 
Fit side-chains
  outliers start: 104
  outliers final: 60
  residues processed: 398
  average time/residue: 0.3558
  time to fit residues: 227.4236
Evaluate side-chains
  300 residues out of total 2722 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 240
  time to evaluate  : 2.775 
Switching outliers to nearest non-outliers
  outliers start: 60
  outliers final: 0
  residues processed: 60
  average time/residue: 0.2456
  time to fit residues: 30.8350
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 312
   random chunks:
   chunk 263 optimal weight:    1.9990
   chunk 236 optimal weight:    2.9990
   chunk 131 optimal weight:    3.9990
   chunk 80 optimal weight:    5.9990
   chunk 159 optimal weight:    2.9990
   chunk 126 optimal weight:    5.9990
   chunk 244 optimal weight:    4.9990
   chunk 94 optimal weight:    0.8980
   chunk 148 optimal weight:    0.9990
   chunk 182 optimal weight:    9.9990
   chunk 283 optimal weight:   20.0000
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
C 165 ASN
C 448 ASN
C 450 ASN
C 481 ASN
C 613 GLN
C 752 GLN
C 798 ASN
C 952 ASN
** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1007 GLN
C1045 HIS
B 409 GLN
B 655 HIS
B 798 ASN
B 952 ASN
** B 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 606 ASN
A 616 ASN
A 675 GLN
A 917 GLN
A 952 ASN
A 989 GLN
A1068 GLN

Total number of N/Q/H flips: 21

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.1173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  25379  Z= 0.206
  Angle     :  0.606  11.254  34483  Z= 0.314
  Chirality :  0.048   0.491   3974
  Planarity :  0.005   0.060   4419
  Dihedral  :  7.733  82.317   3949
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 17.40 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.93 (0.13), residues: 3063
  helix: -0.59 (0.20), residues: 657
  sheet: -1.02 (0.19), residues: 681
  loop : -3.04 (0.12), residues: 1725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP B  64 
   HIS   0.003   0.001   HIS A1045 
   PHE   0.016   0.001   PHE A 342 
   TYR   0.027   0.001   TYR B 170 
   ARG   0.005   0.000   ARG B 357 

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

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

  6126 Ramachandran restraints generated.
    3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6126 Ramachandran restraints generated.
    3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 2722 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 83
    poor density    : 252
  time to evaluate  : 2.663 
Fit side-chains
  outliers start: 83
  outliers final: 46
  residues processed: 315
  average time/residue: 0.3539
  time to fit residues: 183.4411
Evaluate side-chains
  270 residues out of total 2722 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 224
  time to evaluate  : 2.757 
Switching outliers to nearest non-outliers
  outliers start: 46
  outliers final: 0
  residues processed: 46
  average time/residue: 0.2270
  time to fit residues: 23.8733
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 312
   random chunks:
   chunk 157 optimal weight:    0.7980
   chunk 87 optimal weight:    3.9990
   chunk 235 optimal weight:    7.9990
   chunk 192 optimal weight:    5.9990
   chunk 78 optimal weight:    7.9990
   chunk 283 optimal weight:   20.0000
   chunk 306 optimal weight:    5.9990
   chunk 252 optimal weight:    9.9990
   chunk 281 optimal weight:    8.9990
   chunk 96 optimal weight:    9.9990
   chunk 227 optimal weight:    6.9990
   overall best weight:    4.7588

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

Flipped N/Q/H residues before XYZ refinement:
C 448 ASN
** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 613 GLN
C 798 ASN
B 606 ASN
B 798 ASN
B1122 ASN
A  81 ASN
A 115 GLN
A 207 HIS
A 487 ASN
A 606 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  25379  Z= 0.405
  Angle     :  0.721  10.140  34483  Z= 0.376
  Chirality :  0.051   0.301   3974
  Planarity :  0.005   0.074   4419
  Dihedral  :  7.797  80.779   3949
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.68 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.32 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.73 (0.14), residues: 3063
  helix: -0.65 (0.20), residues: 668
  sheet: -0.75 (0.20), residues: 671
  loop : -2.87 (0.12), residues: 1724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.002   TRP A 353 
   HIS   0.005   0.001   HIS B1061 
   PHE   0.019   0.002   PHE B 201 
   TYR   0.034   0.002   TYR B  37 
   ARG   0.005   0.001   ARG B 357 

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

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

  6126 Ramachandran restraints generated.
    3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6126 Ramachandran restraints generated.
    3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 2722 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 75
    poor density    : 227
  time to evaluate  : 2.957 
Fit side-chains
   revert: symmetry clash
  outliers start: 75
  outliers final: 43
  residues processed: 285
  average time/residue: 0.3712
  time to fit residues: 172.7844
Evaluate side-chains
  254 residues out of total 2722 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 211
  time to evaluate  : 2.635 
Switching outliers to nearest non-outliers
  outliers start: 43
  outliers final: 0
  residues processed: 43
  average time/residue: 0.2468
  time to fit residues: 23.2551
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 312
   random chunks:
   chunk 280 optimal weight:    5.9990
   chunk 213 optimal weight:    7.9990
   chunk 147 optimal weight:    8.9990
   chunk 31 optimal weight:    0.1980
   chunk 135 optimal weight:    0.0020
   chunk 190 optimal weight:    0.5980
   chunk 284 optimal weight:    6.9990
   chunk 301 optimal weight:    3.9990
   chunk 148 optimal weight:    2.9990
   chunk 269 optimal weight:   10.0000
   chunk 81 optimal weight:    0.3980
   overall best weight:    0.8390

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

Flipped N/Q/H residues before XYZ refinement:
C 474 GLN
C 613 GLN
C 850 GLN
C 898 GLN
B 414 GLN
B 606 ASN
B 613 GLN
B 798 ASN
B1080 HIS
A 207 HIS
A 239 GLN
A 898 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.1968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  25379  Z= 0.136
  Angle     :  0.521  10.166  34483  Z= 0.274
  Chirality :  0.044   0.170   3974
  Planarity :  0.004   0.059   4419
  Dihedral  :  6.745  74.294   3949
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 19.43 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.07 (0.14), residues: 3063
  helix:  0.15 (0.21), residues: 665
  sheet: -0.38 (0.20), residues: 691
  loop : -2.56 (0.13), residues: 1707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP B 436 
   HIS   0.002   0.000   HIS A  69 
   PHE   0.014   0.001   PHE A  86 
   TYR   0.021   0.001   TYR B  38 
   ARG   0.005   0.000   ARG B 357 

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

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

  6126 Ramachandran restraints generated.
    3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6126 Ramachandran restraints generated.
    3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 2722 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 253
  time to evaluate  : 2.778 
Fit side-chains
  outliers start: 36
  outliers final: 19
  residues processed: 278
  average time/residue: 0.3539
  time to fit residues: 159.8294
Evaluate side-chains
  240 residues out of total 2722 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 221
  time to evaluate  : 2.731 
Switching outliers to nearest non-outliers
  outliers start: 19
  outliers final: 0
  residues processed: 19
  average time/residue: 0.2465
  time to fit residues: 12.3111
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 312
   random chunks:
   chunk 251 optimal weight:    3.9990
   chunk 171 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   chunk 224 optimal weight:    0.4980
   chunk 124 optimal weight:    8.9990
   chunk 257 optimal weight:    7.9990
   chunk 208 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 153 optimal weight:    0.0270
   chunk 270 optimal weight:    5.9990
   chunk 76 optimal weight:    0.4980
   overall best weight:    1.2040

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

Flipped N/Q/H residues before XYZ refinement:
C 271 GLN
C 613 GLN
B 798 ASN
A  69 HIS
A  81 ASN
A 207 HIS
** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  25379  Z= 0.146
  Angle     :  0.517  10.179  34483  Z= 0.270
  Chirality :  0.043   0.206   3974
  Planarity :  0.004   0.061   4419
  Dihedral  :  6.415  68.997   3949
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 19.95 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.14), residues: 3063
  helix:  0.36 (0.21), residues: 667
  sheet: -0.17 (0.20), residues: 664
  loop : -2.39 (0.13), residues: 1732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP B  64 
   HIS   0.002   0.000   HIS B1061 
   PHE   0.016   0.001   PHE A 820 
   TYR   0.022   0.001   TYR A  37 
   ARG   0.006   0.000   ARG B 357 

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

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

  6126 Ramachandran restraints generated.
    3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6126 Ramachandran restraints generated.
    3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 2722 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 237
  time to evaluate  : 2.813 
Fit side-chains
  outliers start: 44
  outliers final: 25
  residues processed: 268
  average time/residue: 0.3541
  time to fit residues: 153.8494
Evaluate side-chains
  250 residues out of total 2722 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 225
  time to evaluate  : 2.850 
Switching outliers to nearest non-outliers
  outliers start: 25
  outliers final: 0
  residues processed: 25
  average time/residue: 0.2325
  time to fit residues: 14.9024
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 312
   random chunks:
   chunk 101 optimal weight:    0.8980
   chunk 271 optimal weight:    0.7980
   chunk 59 optimal weight:    6.9990
   chunk 177 optimal weight:    9.9990
   chunk 74 optimal weight:    0.0770
   chunk 301 optimal weight:    5.9990
   chunk 250 optimal weight:    7.9990
   chunk 139 optimal weight:    0.9980
   chunk 25 optimal weight:   30.0000
   chunk 99 optimal weight:    0.6980
   chunk 158 optimal weight:    8.9990
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
C 613 GLN
B 606 ASN
B1132 ASN
** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  25379  Z= 0.122
  Angle     :  0.486  11.893  34483  Z= 0.254
  Chirality :  0.042   0.166   3974
  Planarity :  0.004   0.060   4419
  Dihedral  :  5.948  62.719   3949
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 20.21 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.15), residues: 3063
  helix:  0.71 (0.21), residues: 665
  sheet: -0.07 (0.20), residues: 666
  loop : -2.21 (0.13), residues: 1732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.001   TRP C 258 
   HIS   0.002   0.000   HIS C 245 
   PHE   0.014   0.001   PHE A 820 
   TYR   0.021   0.001   TYR B 901 
   ARG   0.005   0.000   ARG B 357 

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

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

  6126 Ramachandran restraints generated.
    3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6126 Ramachandran restraints generated.
    3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 2722 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 254
  time to evaluate  : 2.964 
Fit side-chains
  outliers start: 28
  outliers final: 13
  residues processed: 278
  average time/residue: 0.3691
  time to fit residues: 165.6335
Evaluate side-chains
  247 residues out of total 2722 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 234
  time to evaluate  : 2.804 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 0
  residues processed: 13
  average time/residue: 0.2762
  time to fit residues: 10.1135
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 312
   random chunks:
   chunk 291 optimal weight:    9.9990
   chunk 34 optimal weight:    5.9990
   chunk 171 optimal weight:    0.9980
   chunk 220 optimal weight:    1.9990
   chunk 170 optimal weight:    7.9990
   chunk 254 optimal weight:    6.9990
   chunk 168 optimal weight:    6.9990
   chunk 300 optimal weight:    6.9990
   chunk 188 optimal weight:    8.9990
   chunk 183 optimal weight:    3.9990
   chunk 138 optimal weight:    7.9990
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 613 GLN
B  66 HIS
B 798 ASN
A  81 ASN
A 898 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  25379  Z= 0.345
  Angle     :  0.641  15.689  34483  Z= 0.335
  Chirality :  0.048   0.238   3974
  Planarity :  0.005   0.074   4419
  Dihedral  :  6.527  61.356   3949
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 20.61 %
    Favored  : 78.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.14), residues: 3063
  helix:  0.10 (0.20), residues: 668
  sheet: -0.16 (0.20), residues: 670
  loop : -2.30 (0.13), residues: 1725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.002   TRP B  64 
   HIS   0.005   0.001   HIS A1045 
   PHE   0.021   0.002   PHE C 592 
   TYR   0.037   0.002   TYR B  37 
   ARG   0.005   0.001   ARG B 357 

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

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

  6126 Ramachandran restraints generated.
    3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6126 Ramachandran restraints generated.
    3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 2722 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 239
  time to evaluate  : 2.774 
Fit side-chains
  outliers start: 35
  outliers final: 23
  residues processed: 263
  average time/residue: 0.3506
  time to fit residues: 150.1835
Evaluate side-chains
  244 residues out of total 2722 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 221
  time to evaluate  : 2.833 
Switching outliers to nearest non-outliers
  outliers start: 23
  outliers final: 0
  residues processed: 23
  average time/residue: 0.2214
  time to fit residues: 13.5369
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 312
   random chunks:
   chunk 186 optimal weight:    0.9980
   chunk 120 optimal weight:    5.9990
   chunk 179 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 191 optimal weight:    7.9990
   chunk 204 optimal weight:    6.9990
   chunk 148 optimal weight:    4.9990
   chunk 28 optimal weight:    0.6980
   chunk 236 optimal weight:    5.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 613 GLN
B  66 HIS
B 798 ASN
B1098 HIS
** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  25379  Z= 0.221
  Angle     :  0.568  15.228  34483  Z= 0.298
  Chirality :  0.045   0.202   3974
  Planarity :  0.004   0.074   4419
  Dihedral  :  6.326  60.008   3949
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 20.95 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.71 (0.14), residues: 3063
  helix:  0.23 (0.21), residues: 666
  sheet: -0.12 (0.20), residues: 682
  loop : -2.24 (0.13), residues: 1715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.001   TRP B  64 
   HIS   0.006   0.001   HIS B1098 
   PHE   0.017   0.001   PHE C 592 
   TYR   0.026   0.002   TYR A  37 
   ARG   0.005   0.000   ARG B 357 

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

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

  6126 Ramachandran restraints generated.
    3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6126 Ramachandran restraints generated.
    3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 2722 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 225
  time to evaluate  : 2.840 
Fit side-chains
  outliers start: 16
  outliers final: 6
  residues processed: 235
  average time/residue: 0.3821
  time to fit residues: 146.1782
Evaluate side-chains
  225 residues out of total 2722 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 219
  time to evaluate  : 2.848 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.2458
  time to fit residues: 6.8282
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 312
   random chunks:
   chunk 273 optimal weight:    0.9990
   chunk 288 optimal weight:    6.9990
   chunk 262 optimal weight:   10.0000
   chunk 280 optimal weight:    2.9990
   chunk 168 optimal weight:    4.9990
   chunk 122 optimal weight:   10.0000
   chunk 220 optimal weight:    4.9990
   chunk 85 optimal weight:    6.9990
   chunk 253 optimal weight:    5.9990
   chunk 265 optimal weight:    3.9990
   chunk 279 optimal weight:    5.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 613 GLN
B  66 HIS
B 606 ASN
** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  81 ASN
** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  25379  Z= 0.314
  Angle     :  0.634  16.221  34483  Z= 0.332
  Chirality :  0.047   0.237   3974
  Planarity :  0.005   0.079   4419
  Dihedral  :  6.532  58.399   3949
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 21.24 %
    Favored  : 78.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.84 (0.14), residues: 3063
  helix: -0.02 (0.20), residues: 669
  sheet: -0.12 (0.20), residues: 682
  loop : -2.30 (0.13), residues: 1712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.002   TRP A 353 
   HIS   0.004   0.001   HIS A1045 
   PHE   0.021   0.002   PHE C 592 
   TYR   0.033   0.002   TYR B  37 
   ARG   0.005   0.000   ARG B 357 

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

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

  6126 Ramachandran restraints generated.
    3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6126 Ramachandran restraints generated.
    3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 2722 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 219
  time to evaluate  : 2.981 
Fit side-chains
  outliers start: 18
  outliers final: 12
  residues processed: 234
  average time/residue: 0.3621
  time to fit residues: 139.0468
Evaluate side-chains
  228 residues out of total 2722 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 216
  time to evaluate  : 2.971 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 0
  residues processed: 12
  average time/residue: 0.2268
  time to fit residues: 9.2470
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 312
   random chunks:
   chunk 184 optimal weight:    2.9990
   chunk 296 optimal weight:    8.9990
   chunk 180 optimal weight:    0.0570
   chunk 140 optimal weight:    5.9990
   chunk 205 optimal weight:    6.9990
   chunk 310 optimal weight:   10.0000
   chunk 286 optimal weight:    6.9990
   chunk 247 optimal weight:    2.9990
   chunk 25 optimal weight:   40.0000
   chunk 191 optimal weight:    7.9990
   chunk 151 optimal weight:    0.9990
   overall best weight:    2.6106

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

Flipped N/Q/H residues before XYZ refinement:
** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 613 GLN
B  66 HIS
** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  25379  Z= 0.243
  Angle     :  0.585  15.262  34483  Z= 0.308
  Chirality :  0.046   0.207   3974
  Planarity :  0.004   0.075   4419
  Dihedral  :  6.339  55.597   3949
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 21.32 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.14), residues: 3063
  helix:  0.12 (0.20), residues: 666
  sheet: -0.06 (0.20), residues: 677
  loop : -2.24 (0.13), residues: 1720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.002   TRP B  64 
   HIS   0.003   0.001   HIS B1061 
   PHE   0.018   0.002   PHE C 592 
   TYR   0.027   0.002   TYR A  37 
   ARG   0.006   0.000   ARG B 357 

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

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

  6126 Ramachandran restraints generated.
    3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6126 Ramachandran restraints generated.
    3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 2722 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 220
  time to evaluate  : 2.989 
Fit side-chains
  outliers start: 8
  outliers final: 5
  residues processed: 227
  average time/residue: 0.3550
  time to fit residues: 132.3703
Evaluate side-chains
  217 residues out of total 2722 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 212
  time to evaluate  : 2.843 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.2182
  time to fit residues: 5.9275
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 69.4005 > 50:
  distance: 7 - 16:  28.111
  distance: 16 - 17:  19.525
  distance: 16 - 140:  24.967
  distance: 17 - 18:   5.591
  distance: 17 - 20:  33.575
  distance: 18 - 19:   6.040
  distance: 18 - 25:  18.669
  distance: 19 - 137:  33.998
  distance: 20 - 21:  20.482
  distance: 21 - 22:  34.667
  distance: 22 - 23:  27.747
  distance: 25 - 26:  43.871
  distance: 26 - 27:  36.257
  distance: 26 - 29:  10.193
  distance: 27 - 28:  44.450
  distance: 27 - 31:  21.446
  distance: 30 - 136:  32.509
  distance: 31 - 32:  21.147
  distance: 32 - 33:  42.904
  distance: 32 - 35:  33.074
  distance: 33 - 34:  30.507
  distance: 33 - 43:  48.631
  distance: 35 - 36:   8.438
  distance: 36 - 37:  21.841
  distance: 36 - 38:  19.493
  distance: 37 - 39:  13.167
  distance: 38 - 40:  21.446
  distance: 39 - 41:  33.219
  distance: 40 - 41:  48.295
  distance: 41 - 42:   9.076
  distance: 43 - 44:  17.187
  distance: 44 - 45:  21.882
  distance: 45 - 46:  39.140
  distance: 47 - 48:  39.775
  distance: 48 - 51:  23.888
  distance: 49 - 50:   5.490
  distance: 49 - 54:  16.001
  distance: 51 - 52:  42.913
  distance: 51 - 53:  17.890
  distance: 54 - 55:  21.347
  distance: 55 - 56:  47.489
  distance: 55 - 58:  35.323
  distance: 56 - 57:  38.874
  distance: 56 - 60:  58.215
  distance: 58 - 59:  42.216
  distance: 60 - 61:  30.991
  distance: 60 - 66:  15.355
  distance: 61 - 62:  32.551
  distance: 61 - 64:  24.488
  distance: 62 - 63:   7.129
  distance: 62 - 67:   9.209
  distance: 64 - 65:   9.498
  distance: 65 - 66:  17.384
  distance: 67 - 68:  19.810
  distance: 68 - 69:  18.400
  distance: 68 - 71:  30.581
  distance: 69 - 70:  17.570
  distance: 69 - 74:  12.219
  distance: 71 - 72:  44.498
  distance: 71 - 73:  25.578
  distance: 74 - 75:  20.089
  distance: 75 - 76:  31.313
  distance: 75 - 78:  10.753
  distance: 76 - 77:  11.673
  distance: 76 - 83:   8.646
  distance: 78 - 79:  16.176
  distance: 79 - 80:  20.201
  distance: 80 - 81:  22.768
  distance: 81 - 82:  17.412
  distance: 83 - 84:  11.069
  distance: 84 - 85:  12.349
  distance: 84 - 87:  34.027
  distance: 85 - 86:  31.315
  distance: 85 - 91:  20.695
  distance: 87 - 88:  41.681
  distance: 88 - 89:  16.081
  distance: 88 - 90:  16.755