Starting phenix.real_space_refine (version: dev)
on Sat Feb 25 08:20:57 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0z_34419/02_2023/8h0z_34419_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0z_34419/02_2023/8h0z_34419.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0z_34419/02_2023/8h0z_34419.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0z_34419/02_2023/8h0z_34419.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0z_34419/02_2023/8h0z_34419_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0z_34419/02_2023/8h0z_34419_updated.pdb"
  }
  resolution = 2.99
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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
Process input model

  Symmetric amino acids flipped
    Residue "B TYR   41": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR   42": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP   44": "OD1" <-> "OD2"
    Residue "B GLU   45": "OE1" <-> "OE2"
    Residue "B ASP   50": "OD1" <-> "OD2"
    Residue "B ASP   57": "OD1" <-> "OD2"
    Residue "B TYR   63": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  153": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  154": "OD1" <-> "OD2"
    Residue "B TYR  197": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  220": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  312": "OD1" <-> "OD2"
    Residue "B PHE  316": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  545": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  727": "OD1" <-> "OD2"
    Residue "B TYR  738": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  741": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  778": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  812": "OD1" <-> "OD2"
    Residue "B TYR  886": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  932": "OD1" <-> "OD2"
    Residue "B PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP 1121": "OD1" <-> "OD2"
    Residue "A TYR   63": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   69": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  126": "NH1" <-> "NH2"
    Residue "A PHE  153": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  154": "OD1" <-> "OD2"
    Residue "A ARG  183": "NH1" <-> "NH2"
    Residue "A PHE  220": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  252": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  312": "OD1" <-> "OD2"
    Residue "A ASP  454": "OD1" <-> "OD2"
    Residue "A PHE  551": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  553": "NH1" <-> "NH2"
    Residue "A ASP  554": "OD1" <-> "OD2"
    Residue "A TYR  622": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  932": "OD1" <-> "OD2"
    Residue "A GLU  970": "OE1" <-> "OE2"
    Residue "A ASP  976": "OD1" <-> "OD2"
    Residue "A TYR 1120": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU   45": "OE1" <-> "OE2"
    Residue "C PHE   47": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP   57": "OD1" <-> "OD2"
    Residue "C PHE  138": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  153": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  168": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  197": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  200": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  220": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  293": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  294": "OE1" <-> "OE2"
    Residue "C TYR  300": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  312": "OD1" <-> "OD2"
    Residue "C TYR  352": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  501": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  527": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  548": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  578": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  629": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  741": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  778": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  815": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  886": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  918": "OE1" <-> "OE2"
    Residue "C PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP 1100": "OD1" <-> "OD2"
    Residue "C ASP 1121": "OD1" <-> "OD2"
  Time to flip residues: 0.08s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib"
  Total number of atoms: 25047
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "B"
      Number of atoms: 8151
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1045, 8151
          Classifications: {'peptide': 1045}
          Link IDs: {'PTRANS': 50, 'TRANS': 994}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 7992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1022, 7992
          Classifications: {'peptide': 1022}
          Link IDs: {'PTRANS': 49, 'TRANS': 972}
          Chain breaks: 8
    Chain: "C"
      Number of atoms: 8085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1035, 8085
          Classifications: {'peptide': 1035}
          Link IDs: {'PTRANS': 50, 'TRANS': 984}
          Chain breaks: 7
    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 chiralities: 2
    Chain: "E"
      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 chiralities: 2
    Chain: "F"
      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 chiralities: 2
    Chain: "B"
      Number of atoms: 245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 245
          Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 13}
          Classifications: {'undetermined': 15}
          Link IDs: {None: 14}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen chiralities: 13
    Chain: "A"
      Number of atoms: 265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 265
          Unusual residues: {'BLA': 1, 'EIC': 2, 'NAG': 13}
          Classifications: {'undetermined': 16}
          Link IDs: {None: 15}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen chiralities: 13
    Chain: "C"
      Number of atoms: 225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 225
          Unusual residues: {'BLA': 1, 'NAG': 13}
          Classifications: {'undetermined': 14}
          Link IDs: {None: 13}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen chiralities: 13
  Time building chain proxies: 13.53, per 1000 atoms: 0.54
  Number of scatterers: 25047
  At special positions: 0
  Unit cell: (120.45, 125.925, 174.105, 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     140     16.00
     O    4835      8.00
     N    4066      7.00
     C   16006      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=44, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 128 " - pdb=" SG  CYS B 159 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 278 " - pdb=" SG  CYS B 288 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 323 " - pdb=" SG  CYS B 348 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 366 " - pdb=" SG  CYS B 419 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 378 " - pdb=" SG  CYS B 511 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 467 " - pdb=" SG  CYS B 474 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 524 " - pdb=" SG  CYS B 576 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 603 " - pdb=" SG  CYS B 635 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 648 " - pdb=" SG  CYS B 657 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 720 " - pdb=" SG  CYS B 742 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 725 " - pdb=" SG  CYS B 731 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 822 " - pdb=" SG  CYS B 833 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 967 " - pdb=" SG  CYS A 370 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1014 " - pdb=" SG  CYS B1025 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B1064 " - pdb=" SG  CYS B1108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 128 " - pdb=" SG  CYS A 159 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 278 " - pdb=" SG  CYS A 288 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 323 " - pdb=" SG  CYS A 348 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 366 " - pdb=" SG  CYS A 419 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 378 " - pdb=" SG  CYS A 511 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 467 " - pdb=" SG  CYS A 474 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 524 " - pdb=" SG  CYS A 576 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 603 " - pdb=" SG  CYS A 635 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 648 " - pdb=" SG  CYS A 657 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 720 " - pdb=" SG  CYS A 742 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 725 " - pdb=" SG  CYS A 731 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 822 " - pdb=" SG  CYS A 833 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 967 " - pdb=" SG  CYS C 370 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1014 " - pdb=" SG  CYS A1025 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A1064 " - pdb=" SG  CYS A1108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 128 " - pdb=" SG  CYS C 159 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 278 " - pdb=" SG  CYS C 288 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 323 " - pdb=" SG  CYS C 348 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 366 " - pdb=" SG  CYS C 419 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 378 " - pdb=" SG  CYS C 511 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C 467 " - pdb=" SG  CYS C 474 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 524 " - pdb=" SG  CYS C 576 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 603 " - pdb=" SG  CYS C 635 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 648 " - pdb=" SG  CYS C 657 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 720 " - pdb=" SG  CYS C 742 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 725 " - pdb=" SG  CYS C 731 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 822 " - pdb=" SG  CYS C 833 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1014 " - pdb=" SG  CYS C1025 " distance=2.01
    Simple disulfide: pdb=" SG  CYS C1064 " - pdb=" SG  CYS C1108 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A1303 " - " ASN A  65 "
      " NAG A1304 " - " ASN A1080 "
      " NAG A1305 " - " ASN A 109 "
      " NAG A1306 " - " ASN A 119 "
      " NAG A1307 " - " ASN A 158 "
      " NAG A1308 " - " ASN A 269 "
      " NAG A1309 " - " ASN A 318 "
      " NAG A1310 " - " ASN A 357 "
      " NAG A1311 " - " ASN A 602 "
      " NAG A1312 " - " ASN A 691 "
      " NAG A1313 " - " ASN A 699 "
      " NAG A1314 " - " ASN A 783 "
      " NAG A1315 " - " ASN A1056 "
      " NAG B1301 " - " ASN B  65 "
      " NAG B1302 " - " ASN B1080 "
      " NAG B1303 " - " ASN B 109 "
      " NAG B1304 " - " ASN B 119 "
      " NAG B1305 " - " ASN B 158 "
      " NAG B1306 " - " ASN B 269 "
      " NAG B1307 " - " ASN B 318 "
      " NAG B1308 " - " ASN B 357 "
      " NAG B1309 " - " ASN B 602 "
      " NAG B1310 " - " ASN B 691 "
      " NAG B1311 " - " ASN B 699 "
      " NAG B1312 " - " ASN B 783 "
      " NAG B1313 " - " ASN B1056 "
      " NAG C1301 " - " ASN C  65 "
      " NAG C1302 " - " ASN C1080 "
      " NAG C1303 " - " ASN C 109 "
      " NAG C1304 " - " ASN C 119 "
      " NAG C1305 " - " ASN C 158 "
      " NAG C1306 " - " ASN C 318 "
      " NAG C1307 " - " ASN C 357 "
      " NAG C1308 " - " ASN C 602 "
      " NAG C1309 " - " ASN C 691 "
      " NAG C1310 " - " ASN C 699 "
      " NAG C1311 " - " ASN C 783 "
      " NAG C1312 " - " ASN C1056 "
      " NAG C1313 " - " ASN C1116 "
      " NAG D   1 " - " ASN B 227 "
      " NAG E   1 " - " ASN A 227 "
      " NAG F   1 " - " ASN C 227 "
  Time building additional restraints: 9.25
  Conformation dependent library (CDL) restraints added in 3.5 seconds
  

  6112 Ramachandran restraints generated.
    3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5812

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      65 helices and 40 sheets defined
      22.1% alpha, 21.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 4.18
  Creating SS restraints...
    Processing helix  chain 'B' and resid 282 through 290
    Processing helix  chain 'B' and resid 325 through 329
    Processing helix  chain 'B' and resid 352 through 355
    Processing helix  chain 'B' and resid 372 through 376
      removed outlier: 3.848A  pdb=" N   ASN B 375 " --> pdb=" O   THR B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 396
      removed outlier: 4.440A  pdb=" N   ARG B 395 " --> pdb=" O   ASP B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 408
    Processing helix  chain 'B' and resid 489 through 491
      No H-bonds generated for 'chain 'B' and resid 489 through 491'
    Processing helix  chain 'B' and resid 603 through 605
      No H-bonds generated for 'chain 'B' and resid 603 through 605'
    Processing helix  chain 'B' and resid 607 through 610
      No H-bonds generated for 'chain 'B' and resid 607 through 610'
    Processing helix  chain 'B' and resid 612 through 614
      No H-bonds generated for 'chain 'B' and resid 612 through 614'
    Processing helix  chain 'B' and resid 617 through 620
      No H-bonds generated for 'chain 'B' and resid 617 through 620'
    Processing helix  chain 'B' and resid 720 through 724
    Processing helix  chain 'B' and resid 729 through 764
      removed outlier: 4.514A  pdb=" N   GLN B 737 " --> pdb=" O   ASN B 733 " (cutoff:3.500A)
      removed outlier: 4.814A  pdb=" N   TYR B 738 " --> pdb=" O   LEU B 734 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   GLY B 739 " --> pdb=" O   LEU B 735 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   SER B 740 " --> pdb=" O   LEU B 736 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   PHE B 741 " --> pdb=" O   GLN B 737 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   CYS B 742 " --> pdb=" O   TYR B 738 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   THR B 743 " --> pdb=" O   GLY B 739 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   GLN B 744 " --> pdb=" O   SER B 740 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   LEU B 745 " --> pdb=" O   PHE B 741 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 799 through 807
    Processing helix  chain 'B' and resid 819 through 823
    Processing helix  chain 'B' and resid 831 through 837
    Processing helix  chain 'B' and resid 849 through 865
    Processing helix  chain 'B' and resid 880 through 891
    Processing helix  chain 'B' and resid 895 through 900
    Processing helix  chain 'B' and resid 902 through 919
    Processing helix  chain 'B' and resid 925 through 949
      removed outlier: 5.085A  pdb=" N   LYS B 929 " --> pdb=" O   ALA B 926 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   LEU B 930 " --> pdb=" O   LEU B 927 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   GLN B 931 " --> pdb=" O   GLY B 928 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   ASP B 932 " --> pdb=" O   LYS B 929 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   GLN B 947 " --> pdb=" O   LEU B 944 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 959 through 964
    Processing helix  chain 'B' and resid 968 through 1014
      removed outlier: 3.897A  pdb=" N   VAL B 973 " --> pdb=" O   VAL B 969 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   GLN B 974 " --> pdb=" O   GLU B 970 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ALA B 998 " --> pdb=" O   LEU B 994 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   GLU B 999 " --> pdb=" O   ILE B 995 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 290
    Processing helix  chain 'A' and resid 325 through 328
      No H-bonds generated for 'chain 'A' and resid 325 through 328'
    Processing helix  chain 'A' and resid 352 through 355
    Processing helix  chain 'A' and resid 372 through 374
      No H-bonds generated for 'chain 'A' and resid 372 through 374'
    Processing helix  chain 'A' and resid 394 through 396
      No H-bonds generated for 'chain 'A' and resid 394 through 396'
    Processing helix  chain 'A' and resid 404 through 408
    Processing helix  chain 'A' and resid 489 through 491
      No H-bonds generated for 'chain 'A' and resid 489 through 491'
    Processing helix  chain 'A' and resid 720 through 724
    Processing helix  chain 'A' and resid 729 through 737
      removed outlier: 4.045A  pdb=" N   GLN A 737 " --> pdb=" O   ASN A 733 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 742 through 764
      removed outlier: 3.791A  pdb=" N   ALA A 748 " --> pdb=" O   GLN A 744 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   THR A 760 " --> pdb=" O   GLN A 756 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 787
      No H-bonds generated for 'chain 'A' and resid 785 through 787'
    Processing helix  chain 'A' and resid 799 through 807
    Processing helix  chain 'A' and resid 831 through 837
    Processing helix  chain 'A' and resid 849 through 863
      removed outlier: 3.524A  pdb=" N   THR A 863 " --> pdb=" O   LEU A 859 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 880 through 891
      removed outlier: 3.683A  pdb=" N   ILE A 891 " --> pdb=" O   ARG A 887 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 895 through 899
    Processing helix  chain 'A' and resid 902 through 921
    Processing helix  chain 'A' and resid 928 through 949
      removed outlier: 3.850A  pdb=" N   VAL A 945 " --> pdb=" O   LEU A 941 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LYS A 946 " --> pdb=" O   ASN A 942 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLN A 947 " --> pdb=" O   THR A 943 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   LEU A 948 " --> pdb=" O   LEU A 944 " (cutoff:3.500A)
      removed outlier: 4.891A  pdb=" N   SER A 949 " --> pdb=" O   VAL A 945 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 959 through 965
    Processing helix  chain 'A' and resid 968 through 1014
      removed outlier: 3.649A  pdb=" N   ASP A 976 " --> pdb=" O   GLU A 972 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ARG A 977 " --> pdb=" O   VAL A 973 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   LEU A 978 " --> pdb=" O   GLN A 974 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ALA A 998 " --> pdb=" O   LEU A 994 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLU A 999 " --> pdb=" O   ILE A 995 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   SER A1012 " --> pdb=" O   ALA A1008 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 282 through 290
    Processing helix  chain 'C' and resid 325 through 329
    Processing helix  chain 'C' and resid 352 through 356
    Processing helix  chain 'C' and resid 372 through 375
      removed outlier: 4.100A  pdb=" N   ASN C 375 " --> pdb=" O   THR C 372 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 372 through 375'
    Processing helix  chain 'C' and resid 391 through 396
      removed outlier: 3.923A  pdb=" N   VAL C 394 " --> pdb=" O   GLY C 391 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   ARG C 395 " --> pdb=" O   ASP C 392 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 408
      removed outlier: 3.502A  pdb=" N   TYR C 408 " --> pdb=" O   VAL C 404 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 404 through 408'
    Processing helix  chain 'C' and resid 489 through 491
      No H-bonds generated for 'chain 'C' and resid 489 through 491'
    Processing helix  chain 'C' and resid 607 through 610
      No H-bonds generated for 'chain 'C' and resid 607 through 610'
    Processing helix  chain 'C' and resid 617 through 621
    Processing helix  chain 'C' and resid 720 through 723
      No H-bonds generated for 'chain 'C' and resid 720 through 723'
    Processing helix  chain 'C' and resid 729 through 737
      removed outlier: 4.059A  pdb=" N   GLN C 737 " --> pdb=" O   ASN C 733 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 743 through 764
    Processing helix  chain 'C' and resid 785 through 787
      No H-bonds generated for 'chain 'C' and resid 785 through 787'
    Processing helix  chain 'C' and resid 799 through 805
    Processing helix  chain 'C' and resid 831 through 837
    Processing helix  chain 'C' and resid 849 through 865
    Processing helix  chain 'C' and resid 880 through 891
    Processing helix  chain 'C' and resid 895 through 900
    Processing helix  chain 'C' and resid 902 through 920
    Processing helix  chain 'C' and resid 929 through 949
      removed outlier: 3.828A  pdb=" N   VAL C 933 " --> pdb=" O   LYS C 929 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   LEU C 948 " --> pdb=" O   LEU C 944 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   SER C 949 " --> pdb=" O   VAL C 945 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 959 through 964
    Processing helix  chain 'C' and resid 968 through 1014
      removed outlier: 4.173A  pdb=" N   VAL C 973 " --> pdb=" O   VAL C 969 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   GLN C 974 " --> pdb=" O   GLU C 970 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ASP C 976 " --> pdb=" O   GLU C 972 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ALA C 998 " --> pdb=" O   LEU C 994 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLU C 999 " --> pdb=" O   ILE C 995 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'B' and resid 32 through 34
      removed outlier: 3.791A  pdb=" N   VAL B  66 " --> pdb=" O   HIS B  33 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   ASN B  65 " --> pdb=" O   TYR B 256 " (cutoff:3.500A)
      removed outlier: 5.103A  pdb=" N   TYR B 256 " --> pdb=" O   ASN B  65 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ILE B 203 " --> pdb=" O   LYS B 180 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   PHE B 220 " --> pdb=" O   VAL B 196 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   LYS B 198 " --> pdb=" O   PRO B 218 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 52 through 59
    Processing sheet with id=  C, first strand: chain 'B' and resid 230 through 233
      removed outlier: 3.748A  pdb=" N   PHE B 161 " --> pdb=" O   ALA B 127 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 298 through 301
      removed outlier: 4.465A  pdb=" N   GLY B 580 " --> pdb=" O   GLN B 599 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 312 through 315
      removed outlier: 6.718A  pdb=" N   ASN B 526 " --> pdb=" O   VAL B 313 " (cutoff:3.500A)
      removed outlier: 8.313A  pdb=" N   ARG B 315 " --> pdb=" O   ASN B 526 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   ASN B 528 " --> pdb=" O   ARG B 315 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 341 through 345
      removed outlier: 3.576A  pdb=" N   GLU B 341 " --> pdb=" O   SER B 386 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   VAL B 382 " --> pdb=" O   ILE B 345 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ASN B 381 " --> pdb=" O   GLU B 502 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 348 through 350
    Processing sheet with id=  H, first strand: chain 'B' and resid 439 through 441
    Processing sheet with id=  I, first strand: chain 'B' and resid 537 through 540
      removed outlier: 5.340A  pdb=" N   ASP B 560 " --> pdb=" O   ILE B 573 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   GLY B 552 " --> pdb=" O   ASP B 560 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'B' and resid 673 through 678
      removed outlier: 6.461A  pdb=" N   ALA B 658 " --> pdb=" O   PRO B 651 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'B' and resid 693 through 697
      removed outlier: 4.383A  pdb=" N   THR B1058 " --> pdb=" O   PHE B1079 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   ALA B1060 " --> pdb=" O   PHE B1077 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   PHE B1077 " --> pdb=" O   ALA B1060 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'B' and resid 700 through 710
      removed outlier: 3.574A  pdb=" N   MET B1032 " --> pdb=" O   VAL B1047 " (cutoff:3.500A)
      removed outlier: 6.007A  pdb=" N   TYR B1049 " --> pdb=" O   HIS B1030 " (cutoff:3.500A)
      removed outlier: 5.858A  pdb=" N   HIS B1030 " --> pdb=" O   TYR B1049 " (cutoff:3.500A)
    Processing sheet with id=  M, first strand: chain 'B' and resid 715 through 718
      removed outlier: 4.547A  pdb=" N   LYS B 715 " --> pdb=" O   LEU B 843 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'B' and resid 1070 through 1072
    Processing sheet with id=  O, first strand: chain 'A' and resid 32 through 35
      removed outlier: 7.653A  pdb=" N   ASN A  65 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   TYR A 256 " --> pdb=" O   ASN A  65 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   PHE A 220 " --> pdb=" O   VAL A 196 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   LYS A 198 " --> pdb=" O   PRO A 218 " (cutoff:3.500A)
    Processing sheet with id=  P, first strand: chain 'A' and resid 54 through 59
      removed outlier: 4.181A  pdb=" N   ASP A 274 " --> pdb=" O   LYS A 265 " (cutoff:3.500A)
    Processing sheet with id=  Q, first strand: chain 'A' and resid 230 through 233
    Processing sheet with id=  R, first strand: chain 'A' and resid 298 through 302
      removed outlier: 4.520A  pdb=" N   VAL A 581 " --> pdb=" O   THR A 302 " (cutoff:3.500A)
    Processing sheet with id=  S, first strand: chain 'A' and resid 312 through 315
      removed outlier: 8.325A  pdb=" N   VAL A 313 " --> pdb=" O   CYS A 524 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   ASN A 526 " --> pdb=" O   VAL A 313 " (cutoff:3.500A)
      removed outlier: 7.909A  pdb=" N   ARG A 315 " --> pdb=" O   ASN A 526 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ASN A 528 " --> pdb=" O   ARG A 315 " (cutoff:3.500A)
      removed outlier: 4.793A  pdb=" N   ASP A 560 " --> pdb=" O   ILE A 573 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   GLY A 552 " --> pdb=" O   ASP A 560 " (cutoff:3.500A)
    Processing sheet with id=  T, first strand: chain 'A' and resid 341 through 345
      removed outlier: 4.243A  pdb=" N   VAL A 382 " --> pdb=" O   ILE A 345 " (cutoff:3.500A)
    Processing sheet with id=  U, first strand: chain 'A' and resid 439 through 441
    Processing sheet with id=  V, first strand: chain 'A' and resid 673 through 678
      removed outlier: 6.600A  pdb=" N   ALA A 658 " --> pdb=" O   PRO A 651 " (cutoff:3.500A)
    Processing sheet with id=  W, first strand: chain 'A' and resid 693 through 697
      removed outlier: 4.068A  pdb=" N   THR A1058 " --> pdb=" O   PHE A1079 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ALA A1060 " --> pdb=" O   PHE A1077 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   PHE A1077 " --> pdb=" O   ALA A1060 " (cutoff:3.500A)
    Processing sheet with id=  X, first strand: chain 'A' and resid 699 through 710
      removed outlier: 6.251A  pdb=" N   TYR A1049 " --> pdb=" O   HIS A1030 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   HIS A1030 " --> pdb=" O   TYR A1049 " (cutoff:3.500A)
    Processing sheet with id=  Y, first strand: chain 'A' and resid 715 through 718
      removed outlier: 4.472A  pdb=" N   LYS A 715 " --> pdb=" O   LEU A 843 " (cutoff:3.500A)
    Processing sheet with id=  Z, first strand: chain 'A' and resid 1070 through 1072
    Processing sheet with id= AA, first strand: chain 'A' and resid 38 through 41
      removed outlier: 8.537A  pdb=" N   ASN A 214 " --> pdb=" O   GLY A  39 " (cutoff:3.500A)
      removed outlier: 5.977A  pdb=" N   TYR A  41 " --> pdb=" O   ASN A 214 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   LEU A 216 " --> pdb=" O   TYR A  41 " (cutoff:3.500A)
  No H-bonds generated for sheet with id= AA
    Processing sheet with id= AB, first strand: chain 'C' and resid 32 through 34
      removed outlier: 3.759A  pdb=" N   VAL C  66 " --> pdb=" O   HIS C  33 " (cutoff:3.500A)
      removed outlier: 7.638A  pdb=" N   ASN C  65 " --> pdb=" O   TYR C 256 " (cutoff:3.500A)
      removed outlier: 5.047A  pdb=" N   TYR C 256 " --> pdb=" O   ASN C  65 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   LYS C 180 " --> pdb=" O   ILE C 203 " (cutoff:3.500A)
      removed outlier: 6.086A  pdb=" N   LYS C 198 " --> pdb=" O   PRO C 218 " (cutoff:3.500A)
    Processing sheet with id= AC, first strand: chain 'C' and resid 51 through 59
      removed outlier: 3.795A  pdb=" N   THR C  51 " --> pdb=" O   TYR C 266 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   TYR C  53 " --> pdb=" O   LEU C 264 " (cutoff:3.500A)
    Processing sheet with id= AD, first strand: chain 'C' and resid 230 through 233
      removed outlier: 4.248A  pdb=" N   PHE C 161 " --> pdb=" O   ALA C 127 " (cutoff:3.500A)
    Processing sheet with id= AE, first strand: chain 'C' and resid 298 through 301
    Processing sheet with id= AF, first strand: chain 'C' and resid 312 through 315
      removed outlier: 6.441A  pdb=" N   ASN C 526 " --> pdb=" O   VAL C 313 " (cutoff:3.500A)
      removed outlier: 8.008A  pdb=" N   ARG C 315 " --> pdb=" O   ASN C 526 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   ASN C 528 " --> pdb=" O   ARG C 315 " (cutoff:3.500A)
    Processing sheet with id= AG, first strand: chain 'C' and resid 341 through 344
      removed outlier: 3.609A  pdb=" N   GLU C 341 " --> pdb=" O   SER C 386 " (cutoff:3.500A)
    Processing sheet with id= AH, first strand: chain 'C' and resid 439 through 441
    Processing sheet with id= AI, first strand: chain 'C' and resid 537 through 540
    Processing sheet with id= AJ, first strand: chain 'C' and resid 673 through 678
      removed outlier: 6.596A  pdb=" N   ALA C 658 " --> pdb=" O   PRO C 651 " (cutoff:3.500A)
    Processing sheet with id= AK, first strand: chain 'C' and resid 693 through 697
      removed outlier: 3.917A  pdb=" N   THR C1058 " --> pdb=" O   PHE C1079 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ALA C1060 " --> pdb=" O   PHE C1077 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   PHE C1077 " --> pdb=" O   ALA C1060 " (cutoff:3.500A)
    Processing sheet with id= AL, first strand: chain 'C' and resid 700 through 710
      removed outlier: 3.516A  pdb=" N   MET C1032 " --> pdb=" O   VAL C1047 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   TYR C1049 " --> pdb=" O   HIS C1030 " (cutoff:3.500A)
      removed outlier: 5.864A  pdb=" N   HIS C1030 " --> pdb=" O   TYR C1049 " (cutoff:3.500A)
    Processing sheet with id= AM, first strand: chain 'C' and resid 715 through 718
      removed outlier: 4.503A  pdb=" N   LYS C 715 " --> pdb=" O   LEU C 843 " (cutoff:3.500A)
    Processing sheet with id= AN, first strand: chain 'C' and resid 1070 through 1072

    861 hydrogen bonds defined for protein.
    2334 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 10.05

  Time building geometry restraints manager: 10.01 seconds

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

  Histogram of bond lengths:
        1.18 -     1.32: 4052
        1.32 -     1.45: 8141
        1.45 -     1.59: 13233
        1.59 -     1.73: 0
        1.73 -     1.87: 187
  Bond restraints: 25613
  Sorted by residual:
  bond pdb=" ND  BLA C1314 "
       pdb=" C1D BLA C1314 "
    ideal  model  delta    sigma   weight residual
    1.319  1.488 -0.169 2.00e-02 2.50e+03 7.14e+01
  bond pdb=" ND  BLA A1316 "
       pdb=" C1D BLA A1316 "
    ideal  model  delta    sigma   weight residual
    1.319  1.485 -0.166 2.00e-02 2.50e+03 6.92e+01
  bond pdb=" C1C BLA C1314 "
       pdb=" NC  BLA C1314 "
    ideal  model  delta    sigma   weight residual
    1.368  1.532 -0.164 2.00e-02 2.50e+03 6.74e+01
  bond pdb=" C1C BLA B1314 "
       pdb=" NC  BLA B1314 "
    ideal  model  delta    sigma   weight residual
    1.368  1.532 -0.164 2.00e-02 2.50e+03 6.71e+01
  bond pdb=" ND  BLA B1314 "
       pdb=" C1D BLA B1314 "
    ideal  model  delta    sigma   weight residual
    1.319  1.482 -0.163 2.00e-02 2.50e+03 6.61e+01
  ... (remaining 25608 not shown)

  Histogram of bond angle deviations from ideal:
       93.56 -   101.67: 45
      101.67 -   109.79: 3840
      109.79 -   117.91: 15261
      117.91 -   126.03: 15343
      126.03 -   134.15: 328
  Bond angle restraints: 34817
  Sorted by residual:
  angle pdb=" CA  CYS A 159 "
        pdb=" CB  CYS A 159 "
        pdb=" SG  CYS A 159 "
      ideal   model   delta    sigma   weight residual
     114.40  130.79  -16.39 2.30e+00 1.89e-01 5.08e+01
  angle pdb=" CA  CYS C 159 "
        pdb=" CB  CYS C 159 "
        pdb=" SG  CYS C 159 "
      ideal   model   delta    sigma   weight residual
     114.40  127.07  -12.67 2.30e+00 1.89e-01 3.04e+01
  angle pdb=" N   ASP B  50 "
        pdb=" CA  ASP B  50 "
        pdb=" C   ASP B  50 "
      ideal   model   delta    sigma   weight residual
     110.91  104.51    6.40 1.17e+00 7.31e-01 2.99e+01
  angle pdb=" N   CYS A 128 "
        pdb=" CA  CYS A 128 "
        pdb=" C   CYS A 128 "
      ideal   model   delta    sigma   weight residual
     108.45  115.16   -6.71 1.26e+00 6.30e-01 2.84e+01
  angle pdb=" C   ASP B 208 "
        pdb=" N   LEU B 209 "
        pdb=" CA  LEU B 209 "
      ideal   model   delta    sigma   weight residual
     120.67  127.28   -6.61 1.34e+00 5.57e-01 2.43e+01
  ... (remaining 34812 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 13962
       17.89 -    35.77: 959
       35.77 -    53.66: 161
       53.66 -    71.55: 31
       71.55 -    89.43: 12
  Dihedral angle restraints: 15125
    sinusoidal: 6090
      harmonic: 9035
  Sorted by residual:
  dihedral pdb=" CA  TYR A 622 "
           pdb=" C   TYR A 622 "
           pdb=" N   SER A 623 "
           pdb=" CA  SER A 623 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -133.81  -46.19     0      5.00e+00 4.00e-02 8.53e+01
  dihedral pdb=" CA  PHE B  83 "
           pdb=" C   PHE B  83 "
           pdb=" N   LYS B  84 "
           pdb=" CA  LYS B  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -137.93  -42.07     0      5.00e+00 4.00e-02 7.08e+01
  dihedral pdb=" CA  VAL A 206 "
           pdb=" C   VAL A 206 "
           pdb=" N   ARG A 207 "
           pdb=" CA  ARG A 207 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  138.89   41.11     0      5.00e+00 4.00e-02 6.76e+01
  ... (remaining 15122 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.130: 3933
       0.130 -    0.260: 94
       0.260 -    0.390: 5
       0.390 -    0.519: 1
       0.519 -    0.649: 1
  Chirality restraints: 4034
  Sorted by residual:
  chirality pdb=" C1  NAG B1308 "
            pdb=" ND2 ASN B 357 "
            pdb=" C2  NAG B1308 "
            pdb=" O5  NAG B1308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.75   -0.65 2.00e-01 2.50e+01 1.05e+01
  chirality pdb=" C1  NAG B1309 "
            pdb=" ND2 ASN B 602 "
            pdb=" C2  NAG B1309 "
            pdb=" O5  NAG B1309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.00   -0.40 2.00e-01 2.50e+01 4.00e+00
  chirality pdb=" C1  NAG B1306 "
            pdb=" ND2 ASN B 269 "
            pdb=" C2  NAG B1306 "
            pdb=" O5  NAG B1306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.04   -0.36 2.00e-01 2.50e+01 3.15e+00
  ... (remaining 4031 not shown)

  Planarity restraints: 4475
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C BLA C1314 "    0.038 2.00e-02 2.50e+03   2.02e-01 1.02e+03
        pdb=" C1D BLA C1314 "    0.478 2.00e-02 2.50e+03
        pdb=" C2C BLA C1314 "    0.021 2.00e-02 2.50e+03
        pdb=" C3C BLA C1314 "   -0.099 2.00e-02 2.50e+03
        pdb=" C4C BLA C1314 "   -0.162 2.00e-02 2.50e+03
        pdb=" CAC BLA C1314 "   -0.148 2.00e-02 2.50e+03
        pdb=" CHD BLA C1314 "   -0.289 2.00e-02 2.50e+03
        pdb=" CMC BLA C1314 "    0.116 2.00e-02 2.50e+03
        pdb=" NC  BLA C1314 "   -0.083 2.00e-02 2.50e+03
        pdb=" OC  BLA C1314 "    0.128 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" ND  BLA C1314 "    0.161 2.00e-02 2.50e+03   1.87e-01 8.75e+02
        pdb=" C1A BLA C1314 "   -0.428 2.00e-02 2.50e+03
        pdb=" C1D BLA C1314 "    0.024 2.00e-02 2.50e+03
        pdb=" C2D BLA C1314 "   -0.043 2.00e-02 2.50e+03
        pdb=" C3D BLA C1314 "    0.042 2.00e-02 2.50e+03
        pdb=" C4D BLA C1314 "    0.169 2.00e-02 2.50e+03
        pdb=" CAD BLA C1314 "    0.007 2.00e-02 2.50e+03
        pdb=" CHA BLA C1314 "    0.273 2.00e-02 2.50e+03
        pdb=" CHD BLA C1314 "   -0.023 2.00e-02 2.50e+03
        pdb=" CMD BLA C1314 "   -0.181 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" NB  BLA A1316 "    0.104 2.00e-02 2.50e+03   1.10e-01 3.05e+02
        pdb=" OB  BLA A1316 "   -0.010 2.00e-02 2.50e+03
        pdb=" C1B BLA A1316 "    0.101 2.00e-02 2.50e+03
        pdb=" C2B BLA A1316 "    0.021 2.00e-02 2.50e+03
        pdb=" C3B BLA A1316 "   -0.026 2.00e-02 2.50e+03
        pdb=" C4A BLA A1316 "   -0.251 2.00e-02 2.50e+03
        pdb=" C4B BLA A1316 "    0.019 2.00e-02 2.50e+03
        pdb=" CAB BLA A1316 "   -0.109 2.00e-02 2.50e+03
        pdb=" CHB BLA A1316 "    0.156 2.00e-02 2.50e+03
        pdb=" CMB BLA A1316 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 4472 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 4010
        2.76 -     3.30: 21457
        3.30 -     3.83: 38673
        3.83 -     4.37: 46147
        4.37 -     4.90: 82741
  Nonbonded interactions: 193028
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  41 "
            pdb=" O   LEU A  58 "
     model   vdw
     2.229 2.440
  nonbonded pdb=" OG1 THR A 894 "
            pdb=" OD1 ASN A 896 "
     model   vdw
     2.240 2.440
  nonbonded pdb=" OE1 GLN B 947 "
            pdb=" OG  SER B 985 "
     model   vdw
     2.285 2.440
  nonbonded pdb=" NZ  LYS A 793 "
            pdb=" OG1 THR A 795 "
     model   vdw
     2.308 2.520
  nonbonded pdb=" OG1 THR C 894 "
            pdb=" OD1 ASN C 896 "
     model   vdw
     2.311 2.440
  ... (remaining 193023 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 31 through 138 or resid 152 through 810 or resid 815 throu \ 
gh 1123 or resid 1303 through 1313))
  selection = (chain 'B' and (resid 31 through 138 or resid 152 through 604 or resid 619 throu \ 
gh 810 or resid 815 through 822 or resid 829 through 1123 or resid 1303 through  \ 
1313))
  selection = (chain 'C' and (resid 31 through 604 or resid 619 through 822 or resid 829 throu \ 
gh 1123 or resid 1303 through 1313))
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     140      5.16       5
     C   16006      2.51       5
     N    4066      2.21       5
     O    4835      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             1.340
  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:          9.740
  Check model and map are aligned:         0.420
  Process input model:                     61.820
  Find NCS groups from input model:        1.800
  Set up NCS constraints:                  0.140
  Set refine NCS operators:                0.000
  Set scattering table:                    0.210
  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:12.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   88.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
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      :  0.008   0.169  25613  Z= 0.509
  Angle     :  0.900  16.385  34817  Z= 0.501
  Chirality :  0.055   0.649   4034
  Planarity :  0.008   0.202   4433
  Dihedral  : 12.371  89.435   9181
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.14), residues: 3056
  helix: -0.23 (0.19), residues: 696
  sheet:  0.57 (0.20), residues: 687
  loop : -2.08 (0.12), residues: 1673

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

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

  6112 Ramachandran restraints generated.
    3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6112 Ramachandran restraints generated.
    3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 2687 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 3.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 205
  average time/residue: 1.2413
  time to fit residues: 301.7822
Evaluate side-chains
  137 residues out of total 2687 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 3.181 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 4.3272
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 309
   random chunks:
   chunk 260 optimal weight:    5.9990
   chunk 234 optimal weight:    2.9990
   chunk 129 optimal weight:    0.9990
   chunk 80 optimal weight:    0.6980
   chunk 157 optimal weight:    2.9990
   chunk 125 optimal weight:    0.7980
   chunk 242 optimal weight:    4.9990
   chunk 93 optimal weight:    1.9990
   chunk 147 optimal weight:    0.9990
   chunk 180 optimal weight:    4.9990
   chunk 280 optimal weight:    1.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 931 GLN
A 437 ASN
C 304 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.0680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.061  25613  Z= 0.226
  Angle     :  0.577   9.155  34817  Z= 0.306
  Chirality :  0.047   0.579   4034
  Planarity :  0.005   0.064   4433
  Dihedral  :  6.501  77.342   3676
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer Outliers :  1.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.14), residues: 3056
  helix:  0.45 (0.20), residues: 717
  sheet:  0.64 (0.21), residues: 613
  loop : -1.88 (0.13), residues: 1726

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

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

  6112 Ramachandran restraints generated.
    3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6112 Ramachandran restraints generated.
    3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 2687 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 151
  time to evaluate  : 3.194 
Fit side-chains
   revert: symmetry clash
  outliers start: 33
  outliers final: 12
  residues processed: 171
  average time/residue: 1.1870
  time to fit residues: 244.0193
Evaluate side-chains
  151 residues out of total 2687 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 139
  time to evaluate  : 2.972 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 10
  residues processed: 2
  average time/residue: 0.2150
  time to fit residues: 4.8402
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 309
   random chunks:
   chunk 155 optimal weight:    4.9990
   chunk 87 optimal weight:    0.2980
   chunk 233 optimal weight:    0.7980
   chunk 191 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 281 optimal weight:    4.9990
   chunk 303 optimal weight:    0.5980
   chunk 250 optimal weight:    3.9990
   chunk 278 optimal weight:    1.9990
   chunk 95 optimal weight:    0.4980
   chunk 225 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 931 GLN
B 937 ASN
** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.0954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.036  25613  Z= 0.157
  Angle     :  0.517  10.355  34817  Z= 0.273
  Chirality :  0.045   0.506   4034
  Planarity :  0.004   0.051   4433
  Dihedral  :  6.047  77.854   3676
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer Outliers :  1.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.14), residues: 3056
  helix:  1.01 (0.21), residues: 710
  sheet:  0.70 (0.20), residues: 665
  loop : -1.83 (0.13), residues: 1681

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

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

  6112 Ramachandran restraints generated.
    3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6112 Ramachandran restraints generated.
    3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 2687 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 155
  time to evaluate  : 2.729 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 42
  outliers final: 17
  residues processed: 184
  average time/residue: 1.1465
  time to fit residues: 255.3201
Evaluate side-chains
  156 residues out of total 2687 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 139
  time to evaluate  : 3.048 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 17
  outliers final: 14
  residues processed: 4
  average time/residue: 0.2883
  time to fit residues: 6.0358
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 309
   random chunks:
   chunk 277 optimal weight:    0.2980
   chunk 211 optimal weight:    4.9990
   chunk 145 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 134 optimal weight:    0.5980
   chunk 188 optimal weight:    1.9990
   chunk 282 optimal weight:    1.9990
   chunk 298 optimal weight:    0.0870
   chunk 147 optimal weight:    1.9990
   chunk 267 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.9962

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 889 ASN
B 931 GLN
A 904 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.1063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.039  25613  Z= 0.202
  Angle     :  0.531  11.346  34817  Z= 0.278
  Chirality :  0.045   0.503   4034
  Planarity :  0.004   0.048   4433
  Dihedral  :  5.887  77.390   3676
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer Outliers :  1.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.14), residues: 3056
  helix:  1.14 (0.21), residues: 714
  sheet:  0.69 (0.20), residues: 626
  loop : -1.78 (0.13), residues: 1716

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

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

  6112 Ramachandran restraints generated.
    3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6112 Ramachandran restraints generated.
    3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 2687 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 52
    poor density    : 147
  time to evaluate  : 3.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 52
  outliers final: 23
  residues processed: 185
  average time/residue: 1.0037
  time to fit residues: 229.9313
Evaluate side-chains
  166 residues out of total 2687 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 143
  time to evaluate  : 3.071 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 23
  outliers final: 18
  residues processed: 6
  average time/residue: 0.3808
  time to fit residues: 7.9538
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 309
   random chunks:
   chunk 248 optimal weight:    0.8980
   chunk 169 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0980
   chunk 222 optimal weight:    0.6980
   chunk 123 optimal weight:    3.9990
   chunk 254 optimal weight:    4.9990
   chunk 206 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 152 optimal weight:    2.9990
   chunk 268 optimal weight:    0.8980
   chunk 75 optimal weight:    5.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 HIS
** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 889 ASN
B 931 GLN
A 883 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.052  25613  Z= 0.171
  Angle     :  0.519  11.176  34817  Z= 0.272
  Chirality :  0.044   0.483   4034
  Planarity :  0.004   0.048   4433
  Dihedral  :  5.782  77.693   3676
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer Outliers :  1.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.15), residues: 3056
  helix:  1.27 (0.21), residues: 715
  sheet:  0.71 (0.20), residues: 670
  loop : -1.76 (0.13), residues: 1671

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

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

  6112 Ramachandran restraints generated.
    3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6112 Ramachandran restraints generated.
    3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 2687 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 149
  time to evaluate  : 3.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 47
  outliers final: 26
  residues processed: 186
  average time/residue: 1.0944
  time to fit residues: 248.9353
Evaluate side-chains
  163 residues out of total 2687 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 137
  time to evaluate  : 3.093 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 26
  outliers final: 23
  residues processed: 5
  average time/residue: 0.4980
  time to fit residues: 9.2866
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 309
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 268 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0060
   chunk 175 optimal weight:    5.9990
   chunk 73 optimal weight:    8.9990
   chunk 298 optimal weight:    0.2980
   chunk 248 optimal weight:    0.8980
   chunk 138 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 98 optimal weight:    2.9990
   chunk 156 optimal weight:    0.8980
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
** B  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 112 GLN
B 181 HIS
** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 889 ASN
B 931 GLN
A 883 GLN
A 895 GLN
C 883 GLN
C 937 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.1334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.039  25613  Z= 0.153
  Angle     :  0.507  12.056  34817  Z= 0.263
  Chirality :  0.044   0.456   4034
  Planarity :  0.004   0.047   4433
  Dihedral  :  5.622  77.936   3676
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer Outliers :  1.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.15), residues: 3056
  helix:  1.51 (0.21), residues: 703
  sheet:  0.78 (0.20), residues: 662
  loop : -1.69 (0.13), residues: 1691

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

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

  6112 Ramachandran restraints generated.
    3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6112 Ramachandran restraints generated.
    3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 2687 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 143
  time to evaluate  : 3.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 47
  outliers final: 31
  residues processed: 181
  average time/residue: 1.0696
  time to fit residues: 237.4036
Evaluate side-chains
  163 residues out of total 2687 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 132
  time to evaluate  : 3.120 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 31
  outliers final: 27
  residues processed: 5
  average time/residue: 0.3455
  time to fit residues: 6.9929
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 309
   random chunks:
   chunk 288 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 170 optimal weight:    2.9990
   chunk 218 optimal weight:    2.9990
   chunk 169 optimal weight:    0.3980
   chunk 251 optimal weight:    5.9990
   chunk 166 optimal weight:    2.9990
   chunk 297 optimal weight:    0.9980
   chunk 186 optimal weight:    2.9990
   chunk 181 optimal weight:    4.9990
   chunk 137 optimal weight:    2.9990
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
B 181 HIS
** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 889 ASN
A 129 ASN
A 473 ASN
A 883 GLN
A 895 GLN
C 883 GLN
C1088 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.1289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.045  25613  Z= 0.299
  Angle     :  0.571  12.946  34817  Z= 0.299
  Chirality :  0.047   0.521   4034
  Planarity :  0.004   0.048   4433
  Dihedral  :  5.766  76.789   3676
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer Outliers :  1.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.65 (0.14), residues: 3056
  helix:  1.24 (0.21), residues: 706
  sheet:  0.71 (0.20), residues: 656
  loop : -1.74 (0.13), residues: 1694

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

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

  6112 Ramachandran restraints generated.
    3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6112 Ramachandran restraints generated.
    3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 2687 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 53
    poor density    : 141
  time to evaluate  : 3.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 53
  outliers final: 32
  residues processed: 182
  average time/residue: 1.0559
  time to fit residues: 237.8992
Evaluate side-chains
  168 residues out of total 2687 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 136
  time to evaluate  : 3.178 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 32
  outliers final: 28
  residues processed: 5
  average time/residue: 0.7645
  time to fit residues: 11.6106
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 309
   random chunks:
   chunk 184 optimal weight:    1.9990
   chunk 118 optimal weight:   10.0000
   chunk 177 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 189 optimal weight:    3.9990
   chunk 202 optimal weight:    2.9990
   chunk 147 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 234 optimal weight:    1.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
B 181 HIS
** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 889 ASN
A 473 ASN
A 505 ASN
A 883 GLN
A 895 GLN
C 550 GLN
C 599 GLN
C 937 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.1344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.047  25613  Z= 0.310
  Angle     :  0.586  13.403  34817  Z= 0.306
  Chirality :  0.047   0.555   4034
  Planarity :  0.004   0.049   4433
  Dihedral  :  5.845  76.642   3676
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer Outliers :  1.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.14), residues: 3056
  helix:  1.08 (0.20), residues: 712
  sheet:  0.72 (0.20), residues: 654
  loop : -1.78 (0.13), residues: 1690

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

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

  6112 Ramachandran restraints generated.
    3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6112 Ramachandran restraints generated.
    3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 2687 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 52
    poor density    : 138
  time to evaluate  : 3.052 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 52
  outliers final: 33
  residues processed: 180
  average time/residue: 1.0844
  time to fit residues: 247.0077
Evaluate side-chains
  166 residues out of total 2687 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 133
  time to evaluate  : 3.106 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 33
  outliers final: 29
  residues processed: 5
  average time/residue: 0.4385
  time to fit residues: 7.7428
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 309
   random chunks:
   chunk 270 optimal weight:    5.9990
   chunk 285 optimal weight:    0.0670
   chunk 260 optimal weight:    2.9990
   chunk 277 optimal weight:    5.9990
   chunk 167 optimal weight:    3.9990
   chunk 120 optimal weight:    0.0050
   chunk 217 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 250 optimal weight:    3.9990
   chunk 262 optimal weight:    7.9990
   chunk 276 optimal weight:    0.8980
   overall best weight:    1.3936

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

Flipped N/Q/H residues before XYZ refinement:
B 181 HIS
** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 889 ASN
A 473 ASN
A 505 ASN
A 895 GLN
C 599 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.1373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.043  25613  Z= 0.259
  Angle     :  0.568  14.632  34817  Z= 0.298
  Chirality :  0.046   0.545   4034
  Planarity :  0.004   0.047   4433
  Dihedral  :  5.822  76.789   3676
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer Outliers :  1.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.15), residues: 3056
  helix:  1.14 (0.20), residues: 714
  sheet:  0.68 (0.20), residues: 666
  loop : -1.75 (0.13), residues: 1676

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

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

  6112 Ramachandran restraints generated.
    3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6112 Ramachandran restraints generated.
    3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 2687 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 52
    poor density    : 136
  time to evaluate  : 2.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 52
  outliers final: 32
  residues processed: 181
  average time/residue: 1.0681
  time to fit residues: 239.0850
Evaluate side-chains
  165 residues out of total 2687 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 133
  time to evaluate  : 3.517 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 32
  outliers final: 30
  residues processed: 3
  average time/residue: 0.5551
  time to fit residues: 7.8272
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 309
   random chunks:
   chunk 182 optimal weight:    2.9990
   chunk 293 optimal weight:    3.9990
   chunk 179 optimal weight:    0.8980
   chunk 139 optimal weight:    3.9990
   chunk 204 optimal weight:    3.9990
   chunk 307 optimal weight:    0.5980
   chunk 283 optimal weight:    2.9990
   chunk 245 optimal weight:    0.3980
   chunk 25 optimal weight:    2.9990
   chunk 189 optimal weight:    2.9990
   chunk 150 optimal weight:    2.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 599 GLN
** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 889 ASN
A 473 ASN
A 895 GLN
C 599 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.1423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.044  25613  Z= 0.288
  Angle     :  0.588  14.531  34817  Z= 0.307
  Chirality :  0.047   0.558   4034
  Planarity :  0.004   0.047   4433
  Dihedral  :  5.866  76.275   3676
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer Outliers :  1.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.14), residues: 3056
  helix:  1.09 (0.20), residues: 715
  sheet:  0.64 (0.20), residues: 667
  loop : -1.76 (0.13), residues: 1674

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

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

  6112 Ramachandran restraints generated.
    3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6112 Ramachandran restraints generated.
    3056 Oldfield, 0 Emsley, 3056 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 2687 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 137
  time to evaluate  : 3.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 36
  outliers final: 30
  residues processed: 169
  average time/residue: 1.1421
  time to fit residues: 238.6770
Evaluate side-chains
  161 residues out of total 2687 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 131
  time to evaluate  : 3.138 
Switching outliers to nearest non-outliers
   revert: symmetry clash
  outliers start: 30
  outliers final: 28
  residues processed: 3
  average time/residue: 0.3838
  time to fit residues: 6.2423
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 309
   random chunks:
   chunk 194 optimal weight:    0.5980
   chunk 261 optimal weight:    5.9990
   chunk 75 optimal weight:    0.0470
   chunk 226 optimal weight:    9.9990
   chunk 36 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0870
   chunk 245 optimal weight:    5.9990
   chunk 102 optimal weight:    0.7980
   chunk 252 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   overall best weight:    0.5058

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

Flipped N/Q/H residues before XYZ refinement:
B 181 HIS
** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 599 GLN
** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 883 GLN
B 889 ASN
A 883 GLN
C 550 GLN
C 599 GLN
C 937 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.124442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.089181 restraints weight = 37202.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 2.60
r_work: 0.2930 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2777 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.1550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.039  25613  Z= 0.149
  Angle     :  0.519  13.765  34817  Z= 0.270
  Chirality :  0.044   0.467   4034
  Planarity :  0.004   0.049   4433
  Dihedral  :  5.613  77.352   3676
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer Outliers :  1.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.15), residues: 3056
  helix:  1.46 (0.21), residues: 714
  sheet:  0.70 (0.20), residues: 678
  loop : -1.66 (0.13), residues: 1664

===============================================================================
Job complete
usr+sys time: 5788.93 seconds
wall clock time: 106 minutes 16.75 seconds (6376.75 seconds total)