Starting phenix.real_space_refine
on Sat Sep 28 19:51:28 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sas_40278/09_2024/8sas_40278_neut.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sas_40278/09_2024/8sas_40278.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sas_40278/09_2024/8sas_40278.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sas_40278/09_2024/8sas_40278.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sas_40278/09_2024/8sas_40278_neut.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sas_40278/09_2024/8sas_40278_neut.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.354
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     132      5.16       5
     C   12531      2.51       5
     N    3318      2.21       5
     O    4047      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 20028
  Number of models: 1
  Model: ""
    Number of chains: 24
    Chain: "A"
      Number of atoms: 3615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 462, 3615
          Classifications: {'peptide': 462}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436}
    Chain: "B"
      Number of atoms: 983
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 983
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 1, 'TRANS': 122}
    Chain: "C"
      Number of atoms: 997
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 997
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "D"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 815
          Classifications: {'peptide': 111}
          Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 103}
    Chain: "F"
      Number of atoms: 3615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 462, 3615
          Classifications: {'peptide': 462}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436}
    Chain: "G"
      Number of atoms: 983
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 983
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 1, 'TRANS': 122}
    Chain: "H"
      Number of atoms: 997
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 997
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "I"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 815
          Classifications: {'peptide': 111}
          Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 103}
    Chain: "K"
      Number of atoms: 3615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 462, 3615
          Classifications: {'peptide': 462}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436}
    Chain: "L"
      Number of atoms: 983
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 983
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 1, 'TRANS': 122}
    Chain: "M"
      Number of atoms: 997
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 997
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "N"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 815
          Classifications: {'peptide': 111}
          Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 103}
    Chain: "E"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "J"
      Number of atoms: 105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 105
          Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 9
    Chain: "O"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "P"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "Q"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 72
          Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "R"
      Number of atoms: 127
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 127
          Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 33
          Unresolved non-hydrogen chiralities: 11
    Chain: "S"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "T"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "U"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 72
          Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
    Chain: "V"
      Number of atoms: 105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 105
          Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 9
    Chain: "W"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "X"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 12.85, per 1000 atoms: 0.64
  Number of scatterers: 20028
  At special positions: 0
  Unit cell: (160.966, 162.032, 143.91, 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     132     16.00
     O    4047      8.00
     N    3318      7.00
     C   12531      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=45, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  54 " - pdb=" SG  CYS A  74 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 119 " - pdb=" SG  CYS A 205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 126 " - pdb=" SG  CYS A 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 157 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 201 " - pdb=" SG  CYS A 433 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 218 " - pdb=" SG  CYS A 247 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 228 " - pdb=" SG  CYS A 239 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 296 " - pdb=" SG  CYS A 331 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 378 " - pdb=" SG  CYS A 445 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 385 " - pdb=" SG  CYS A 418 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 501 " - pdb=" SG  CYS B 605 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 598 " - pdb=" SG  CYS B 604 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 252 " - pdb=" SG  CYS D 320 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 321 " - pdb=" SG  CYS D 331 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  54 " - pdb=" SG  CYS F  74 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 119 " - pdb=" SG  CYS F 205 " distance=2.02
    Simple disulfide: pdb=" SG  CYS F 126 " - pdb=" SG  CYS F 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 131 " - pdb=" SG  CYS F 157 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 201 " - pdb=" SG  CYS F 433 " distance=2.01
    Simple disulfide: pdb=" SG  CYS F 218 " - pdb=" SG  CYS F 247 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 228 " - pdb=" SG  CYS F 239 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 296 " - pdb=" SG  CYS F 331 " distance=2.02
    Simple disulfide: pdb=" SG  CYS F 378 " - pdb=" SG  CYS F 445 " distance=2.05
    Simple disulfide: pdb=" SG  CYS F 385 " - pdb=" SG  CYS F 418 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 501 " - pdb=" SG  CYS G 605 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 598 " - pdb=" SG  CYS G 604 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 252 " - pdb=" SG  CYS I 320 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 321 " - pdb=" SG  CYS I 331 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  54 " - pdb=" SG  CYS K  74 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 119 " - pdb=" SG  CYS K 205 " distance=2.04
    Simple disulfide: pdb=" SG  CYS K 126 " - pdb=" SG  CYS K 196 " distance=2.04
    Simple disulfide: pdb=" SG  CYS K 131 " - pdb=" SG  CYS K 157 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 201 " - pdb=" SG  CYS K 433 " distance=2.02
    Simple disulfide: pdb=" SG  CYS K 218 " - pdb=" SG  CYS K 247 " distance=2.02
    Simple disulfide: pdb=" SG  CYS K 228 " - pdb=" SG  CYS K 239 " distance=2.04
    Simple disulfide: pdb=" SG  CYS K 296 " - pdb=" SG  CYS K 331 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 378 " - pdb=" SG  CYS K 445 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 385 " - pdb=" SG  CYS K 418 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K 501 " - pdb=" SG  CYS L 605 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 598 " - pdb=" SG  CYS L 604 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  22 " - pdb=" SG  CYS M  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N 252 " - pdb=" SG  CYS N 320 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N 321 " - pdb=" SG  CYS N 331 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 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
    ALPHA1-2
      " MAN J   4 " - " MAN J   5 "
      " MAN J   5 " - " MAN J   6 "
      " MAN J   8 " - " MAN J   9 "
      " MAN Q   4 " - " MAN Q   5 "
      " MAN R   4 " - " MAN R   5 "
      " MAN R   5 " - " MAN R   6 "
      " MAN R   8 " - " MAN R   9 "
      " MAN R  10 " - " MAN R  11 "
      " MAN U   4 " - " MAN U   5 "
      " MAN V   4 " - " MAN V   5 "
      " MAN V   5 " - " MAN V   6 "
    ALPHA1-3
      " BMA E   3 " - " MAN E   4 "
      " BMA J   3 " - " MAN J   4 "
      " BMA Q   3 " - " MAN Q   4 "
      " BMA R   3 " - " MAN R   4 "
      " MAN R   7 " - " MAN R   8 "
      " BMA U   3 " - " MAN U   4 "
      " BMA V   3 " - " MAN V   4 "
      " MAN V   7 " - " MAN V   8 "
      " BMA X   3 " - " MAN X   4 "
    ALPHA1-6
      " BMA E   3 " - " MAN E   5 "
      " BMA J   3 " - " MAN J   7 "
      " MAN J   7 " - " MAN J   8 "
      " BMA Q   3 " - " MAN Q   6 "
      " BMA R   3 " - " MAN R   7 "
      " MAN R   7 " - " MAN R  10 "
      " BMA U   3 " - " MAN U   6 "
      " BMA V   3 " - " MAN V   7 "
      " MAN V   7 " - " MAN V   9 "
      " BMA W   3 " - " MAN W   4 "
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG J   1 " - " NAG J   2 "
      " NAG J   2 " - " BMA J   3 "
      " NAG O   1 " - " NAG O   2 "
      " NAG O   2 " - " BMA O   3 "
      " NAG P   1 " - " NAG P   2 "
      " NAG P   2 " - " BMA P   3 "
      " NAG Q   1 " - " NAG Q   2 "
      " NAG Q   2 " - " BMA Q   3 "
      " NAG R   1 " - " NAG R   2 "
      " NAG R   2 " - " BMA R   3 "
      " NAG S   1 " - " NAG S   2 "
      " NAG S   2 " - " BMA S   3 "
      " NAG T   1 " - " NAG T   2 "
      " NAG T   2 " - " BMA T   3 "
      " NAG U   1 " - " NAG U   2 "
      " NAG U   2 " - " BMA U   3 "
      " NAG V   1 " - " NAG V   2 "
      " NAG V   2 " - " BMA V   3 "
      " NAG W   1 " - " NAG W   2 "
      " NAG W   2 " - " BMA W   3 "
      " NAG X   1 " - " NAG X   2 "
      " NAG X   2 " - " BMA X   3 "
    NAG-ASN
      " NAG E   1 " - " ASN A 301 "
      " NAG J   1 " - " ASN A 332 "
      " NAG O   1 " - " ASN A 156 "
      " NAG P   1 " - " ASN A 442 "
      " NAG Q   1 " - " ASN F 301 "
      " NAG R   1 " - " ASN F 332 "
      " NAG S   1 " - " ASN F 156 "
      " NAG T   1 " - " ASN F 442 "
      " NAG U   1 " - " ASN K 301 "
      " NAG V   1 " - " ASN K 332 "
      " NAG W   1 " - " ASN K 156 "
      " NAG X   1 " - " ASN K 442 "
  Time building additional restraints: 5.96
  Conformation dependent library (CDL) restraints added in 2.5 seconds
  

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4548

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 46 sheets defined
      17.8% alpha, 24.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 57 through 61
      removed outlier: 3.852A  pdb=" N   ALA A  60 " --> pdb=" O   ASP A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 74
    Processing helix  chain 'A' and resid 99 through 116
      removed outlier: 3.658A  pdb=" N   GLN A 114 " --> pdb=" O   SER A 110 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   LEU A 116 " --> pdb=" O   TRP A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 353
      removed outlier: 3.670A  pdb=" N   GLU A 348 " --> pdb=" O   LYS A 344 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   LYS A 351 " --> pdb=" O   ILE A 347 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   HIS A 352 " --> pdb=" O   GLU A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 480
      removed outlier: 3.568A  pdb=" N   ARG A 480 " --> pdb=" O   ARG A 476 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 530 through 534
      removed outlier: 3.583A  pdb=" N   SER B 534 " --> pdb=" O   GLY B 531 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 537 through 542
    Processing helix  chain 'B' and resid 571 through 577
      removed outlier: 3.667A  pdb=" N   GLN B 575 " --> pdb=" O   TRP B 571 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 580 through 596
      removed outlier: 3.867A  pdb=" N   LEU B 587 " --> pdb=" O   VAL B 583 " (cutoff:3.500A)
      removed outlier: 4.765A  pdb=" N   ARG B 588 " --> pdb=" O   GLU B 584 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   TRP B 596 " --> pdb=" O   LEU B 592 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 611 through 615
    Processing helix  chain 'B' and resid 618 through 625
    Processing helix  chain 'B' and resid 627 through 636
    Processing helix  chain 'B' and resid 638 through 649
    Processing helix  chain 'B' and resid 650 through 654
    Processing helix  chain 'B' and resid 659 through 664
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 3.524A  pdb=" N   THR C  91 " --> pdb=" O   SER C  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 311 through 315
    Processing helix  chain 'F' and resid 99 through 115
      removed outlier: 3.694A  pdb=" N   GLN F 114 " --> pdb=" O   SER F 110 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 177 through 179
      No H-bonds generated for 'chain 'F' and resid 177 through 179'
    Processing helix  chain 'F' and resid 335 through 350
      removed outlier: 4.310A  pdb=" N   ILE F 347 " --> pdb=" O   GLN F 343 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   GLU F 348 " --> pdb=" O   LYS F 344 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU F 349 " --> pdb=" O   VAL F 345 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 387 through 391
    Processing helix  chain 'F' and resid 475 through 484
      removed outlier: 3.654A  pdb=" N   ARG F 480 " --> pdb=" O   ARG F 476 " (cutoff:3.500A)
      removed outlier: 5.939A  pdb=" N   SER F 481 " --> pdb=" O   ASP F 477 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   GLU F 482 " --> pdb=" O   ASN F 478 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 529 through 534
    Processing helix  chain 'G' and resid 537 through 542
      removed outlier: 3.797A  pdb=" N   ALA G 541 " --> pdb=" O   LEU G 537 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 571 through 580
      removed outlier: 5.232A  pdb=" N   ALA G 578 " --> pdb=" O   LYS G 574 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   ARG G 579 " --> pdb=" O   GLN G 575 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   VAL G 580 " --> pdb=" O   LEU G 576 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 580 through 585
      removed outlier: 3.550A  pdb=" N   GLU G 584 " --> pdb=" O   VAL G 580 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 585 through 596
    Processing helix  chain 'G' and resid 618 through 625
      removed outlier: 3.701A  pdb=" N   ILE G 622 " --> pdb=" O   ASN G 618 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 627 through 636
      removed outlier: 3.543A  pdb=" N   TRP G 631 " --> pdb=" O   THR G 627 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 638 through 649
    Processing helix  chain 'G' and resid 649 through 654
    Processing helix  chain 'G' and resid 656 through 663
      removed outlier: 4.538A  pdb=" N   LEU G 663 " --> pdb=" O   ASP G 659 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 30
      No H-bonds generated for 'chain 'H' and resid 28 through 30'
    Processing helix  chain 'H' and resid 88 through 92
      removed outlier: 3.689A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 258 through 262
      removed outlier: 3.777A  pdb=" N   LYS I 261 " --> pdb=" O   ASP I 258 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   PHE I 262 " --> pdb=" O   VAL I 259 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 258 through 262'
    Processing helix  chain 'I' and resid 311 through 315
      removed outlier: 3.540A  pdb=" N   GLU I 315 " --> pdb=" O   VAL I 312 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 69 through 74
      removed outlier: 3.776A  pdb=" N   CYS K  74 " --> pdb=" O   ALA K  70 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 98 through 116
      removed outlier: 4.508A  pdb=" N   ASP K 102 " --> pdb=" O   ASN K  98 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLU K 106 " --> pdb=" O   ASP K 102 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 177 through 179
      No H-bonds generated for 'chain 'K' and resid 177 through 179'
    Processing helix  chain 'K' and resid 334 through 350
    Processing helix  chain 'K' and resid 474 through 484
      removed outlier: 4.455A  pdb=" N   GLU K 482 " --> pdb=" O   ASN K 478 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   TYR K 484 " --> pdb=" O   ARG K 480 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 520 through 524
      removed outlier: 4.145A  pdb=" N   LEU L 523 " --> pdb=" O   LEU L 520 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLY L 524 " --> pdb=" O   GLY L 521 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 520 through 524'
    Processing helix  chain 'L' and resid 571 through 580
      removed outlier: 4.446A  pdb=" N   GLN L 577 " --> pdb=" O   ILE L 573 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   ALA L 578 " --> pdb=" O   LYS L 574 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ARG L 579 " --> pdb=" O   GLN L 575 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 580 through 585
    Processing helix  chain 'L' and resid 585 through 596
      removed outlier: 3.896A  pdb=" N   TRP L 596 " --> pdb=" O   LEU L 592 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 618 through 624
    Processing helix  chain 'L' and resid 627 through 636
    Processing helix  chain 'L' and resid 638 through 650
    Processing helix  chain 'L' and resid 651 through 656
      removed outlier: 3.767A  pdb=" N   ASN L 656 " --> pdb=" O   GLN L 652 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 659 through 663
      removed outlier: 3.810A  pdb=" N   ALA L 662 " --> pdb=" O   ASP L 659 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 28 through 30
      No H-bonds generated for 'chain 'M' and resid 28 through 30'
    Processing helix  chain 'N' and resid 258 through 262
    Processing helix  chain 'N' and resid 311 through 315
    Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 496
      removed outlier: 3.791A  pdb=" N   GLY A 495 " --> pdb=" O   TYR A  39 " (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   VAL B 608 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
      removed outlier: 9.761A  pdb=" N   VAL A  38 " --> pdb=" O   THR B 606 " (cutoff:3.500A)
      removed outlier: 8.177A  pdb=" N   THR B 606 " --> pdb=" O   VAL A  38 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47
    Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92
      removed outlier: 3.502A  pdb=" N   GLU A  91 " --> pdb=" O   CYS A 239 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 173
      removed outlier: 4.572A  pdb=" N   ASN A 156 " --> pdb=" O   SER A 132 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 272 through 273
      removed outlier: 4.250A  pdb=" N   ARG A 273 " --> pdb=" O   ILE A 285 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ILE A 285 " --> pdb=" O   ARG A 273 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   GLU A 293 " --> pdb=" O   SER A 334 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   SER A 334 " --> pdb=" O   GLU A 293 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   PHE A 382 " --> pdb=" O   LYS A 421 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   PHE A 383 " --> pdb=" O   PHE A 376 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   PHE A 376 " --> pdb=" O   PHE A 383 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 272 through 273
      removed outlier: 4.250A  pdb=" N   ARG A 273 " --> pdb=" O   ILE A 285 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ILE A 285 " --> pdb=" O   ARG A 273 " (cutoff:3.500A)
      removed outlier: 7.758A  pdb=" N   THR A 450 " --> pdb=" O   LEU A 288 " (cutoff:3.500A)
      removed outlier: 10.720A  pdb=" N   THR A 290 " --> pdb=" O   ASN A 448 " (cutoff:3.500A)
      removed outlier: 9.712A  pdb=" N   ASN A 448 " --> pdb=" O   THR A 290 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 304 through 308
      removed outlier: 3.549A  pdb=" N   ALA A 319 " --> pdb=" O   LYS A 305 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   VAL A 307 " --> pdb=" O   PHE A 317 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   PHE A 317 " --> pdb=" O   VAL A 307 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 360
      removed outlier: 4.102A  pdb=" N   ILE A 359 " --> pdb=" O   TYR A 395 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   TYR A 395 " --> pdb=" O   ILE A 359 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 425
    Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 12
      removed outlier: 3.610A  pdb=" N   THR C 124 " --> pdb=" O   GLU C  10 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LYS C  12 " --> pdb=" O   THR C 124 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL C  93 " --> pdb=" O   LEU C  39 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   VAL C  37 " --> pdb=" O   TYR C  95 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   TYR C  33 " --> pdb=" O   GLY C  99 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ILE C  34 " --> pdb=" O   TRP C  50 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   TRP C  50 " --> pdb=" O   ILE C  34 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   TRP C  36 " --> pdb=" O   LEU C  48 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ASN C  59 " --> pdb=" O   TRP C  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 20 through 22
      removed outlier: 3.734A  pdb=" N   ALA C  79 " --> pdb=" O   CYS C  22 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 247 through 253
      removed outlier: 3.675A  pdb=" N   ALA D 303 " --> pdb=" O   CYS D 252 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 277 through 281
      removed outlier: 6.215A  pdb=" N   TYR D 278 " --> pdb=" O   GLN D 269 " (cutoff:3.500A)
      removed outlier: 7.606A  pdb=" N   GLN D 269 " --> pdb=" O   TYR D 278 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   ILE D 280 " --> pdb=" O   TRP D 267 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 277 through 281
      removed outlier: 6.215A  pdb=" N   TYR D 278 " --> pdb=" O   GLN D 269 " (cutoff:3.500A)
      removed outlier: 7.606A  pdb=" N   GLN D 269 " --> pdb=" O   TYR D 278 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   ILE D 280 " --> pdb=" O   TRP D 267 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'F' and resid 35 through 40
      removed outlier: 3.710A  pdb=" N   THR F 499 " --> pdb=" O   TRP F  35 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 45 through 47
      removed outlier: 3.568A  pdb=" N   LYS F 487 " --> pdb=" O   LEU F 226 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ILE F 225 " --> pdb=" O   VAL F 245 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL F 245 " --> pdb=" O   ILE F 225 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 75 through 76
      removed outlier: 7.055A  pdb=" N   CYS F  54 " --> pdb=" O   VAL F  75 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 169 through 176
      removed outlier: 3.585A  pdb=" N   ALA F 174 " --> pdb=" O   CYS F 157 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   CYS F 157 " --> pdb=" O   ALA F 174 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   TYR F 191 " --> pdb=" O   LEU F 129 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 259 through 260
      removed outlier: 6.614A  pdb=" N   LEU F 260 " --> pdb=" O   THR F 450 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   VAL F 292 " --> pdb=" O   ILE F 449 " (cutoff:3.500A)
      removed outlier: 7.559A  pdb=" N   GLY F 451 " --> pdb=" O   THR F 290 " (cutoff:3.500A)
      removed outlier: 11.279A  pdb=" N   THR F 290 " --> pdb=" O   GLY F 451 " (cutoff:3.500A)
      removed outlier: 12.407A  pdb=" N   LEU F 453 " --> pdb=" O   LEU F 288 " (cutoff:3.500A)
      removed outlier: 12.321A  pdb=" N   LEU F 288 " --> pdb=" O   LEU F 453 " (cutoff:3.500A)
      removed outlier: 11.092A  pdb=" N   THR F 455 " --> pdb=" O   VAL F 286 " (cutoff:3.500A)
      removed outlier: 11.485A  pdb=" N   VAL F 286 " --> pdb=" O   THR F 455 " (cutoff:3.500A)
      removed outlier: 11.768A  pdb=" N   ASP F 457 " --> pdb=" O   ILE F 284 " (cutoff:3.500A)
      removed outlier: 12.582A  pdb=" N   ILE F 284 " --> pdb=" O   ASP F 457 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   GLU F 293 " --> pdb=" O   SER F 334 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   SER F 334 " --> pdb=" O   GLU F 293 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   PHE F 382 " --> pdb=" O   LYS F 421 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   GLU F 381 " --> pdb=" O   CYS F 378 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   CYS F 378 " --> pdb=" O   GLU F 381 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'F' and resid 271 through 273
      removed outlier: 12.582A  pdb=" N   ILE F 284 " --> pdb=" O   ASP F 457 " (cutoff:3.500A)
      removed outlier: 11.768A  pdb=" N   ASP F 457 " --> pdb=" O   ILE F 284 " (cutoff:3.500A)
      removed outlier: 11.485A  pdb=" N   VAL F 286 " --> pdb=" O   THR F 455 " (cutoff:3.500A)
      removed outlier: 11.092A  pdb=" N   THR F 455 " --> pdb=" O   VAL F 286 " (cutoff:3.500A)
      removed outlier: 12.321A  pdb=" N   LEU F 288 " --> pdb=" O   LEU F 453 " (cutoff:3.500A)
      removed outlier: 12.407A  pdb=" N   LEU F 453 " --> pdb=" O   LEU F 288 " (cutoff:3.500A)
      removed outlier: 11.279A  pdb=" N   THR F 290 " --> pdb=" O   GLY F 451 " (cutoff:3.500A)
      removed outlier: 7.559A  pdb=" N   GLY F 451 " --> pdb=" O   THR F 290 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   VAL F 292 " --> pdb=" O   ILE F 449 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   THR F 467 " --> pdb=" O   ASP F 457 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 304 through 308
    Processing sheet with id=AC4, first strand: chain 'F' and resid 423 through 425
    Processing sheet with id=AC5, first strand: chain 'H' and resid 3 through 6
      removed outlier: 4.040A  pdb=" N   VAL H   5 " --> pdb=" O   ALA H  23 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ALA H  23 " --> pdb=" O   VAL H   5 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.391A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 124 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC6
    Processing sheet with id=AC7, first strand: chain 'H' and resid 59 through 60
      removed outlier: 4.060A  pdb=" N   ASN H  59 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 5.720A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 4.744A  pdb=" N   TYR H  33 " --> pdb=" O   GLY H  99 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   HIS H 116 " --> pdb=" O   THR H  98 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'I' and resid 248 through 253
      removed outlier: 3.597A  pdb=" N   ILE I 248 " --> pdb=" O   ILE I 307 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   SER I 299 " --> pdb=" O   THR I 302 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   SER I 304 " --> pdb=" O   SER I 297 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'I' and resid 277 through 280
      removed outlier: 3.708A  pdb=" N   LEU I 279 " --> pdb=" O   TRP I 267 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   TRP I 267 " --> pdb=" O   LEU I 279 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'I' and resid 277 through 280
      removed outlier: 3.708A  pdb=" N   LEU I 279 " --> pdb=" O   TRP I 267 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   TRP I 267 " --> pdb=" O   LEU I 279 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'K' and resid 495 through 499
      removed outlier: 3.976A  pdb=" N   VAL K  36 " --> pdb=" O   THR L 606 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'K' and resid 45 through 47
    Processing sheet with id=AD4, first strand: chain 'K' and resid 55 through 56
      removed outlier: 4.101A  pdb=" N   SER K  56 " --> pdb=" O   VAL K  75 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD4
    Processing sheet with id=AD5, first strand: chain 'K' and resid 91 through 94
      removed outlier: 4.195A  pdb=" N   GLU K  91 " --> pdb=" O   CYS K 239 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLY K 237 " --> pdb=" O   PHE K  93 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'K' and resid 129 through 130
      removed outlier: 3.546A  pdb=" N   TYR K 191 " --> pdb=" O   LEU K 129 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'K' and resid 155 through 161
      removed outlier: 4.080A  pdb=" N   CYS K 157 " --> pdb=" O   ALA K 174 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ALA K 174 " --> pdb=" O   CYS K 157 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LYS K 170 " --> pdb=" O   THR K 161 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'K' and resid 259 through 260
      removed outlier: 3.770A  pdb=" N   GLY K 451 " --> pdb=" O   LEU K 260 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ARG K 273 " --> pdb=" O   ILE K 285 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'K' and resid 259 through 260
      removed outlier: 3.770A  pdb=" N   GLY K 451 " --> pdb=" O   LEU K 260 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'K' and resid 330 through 333
      removed outlier: 3.692A  pdb=" N   HIS K 330 " --> pdb=" O   THR K 297 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'K' and resid 304 through 309
      removed outlier: 4.014A  pdb=" N   GLN K 315 " --> pdb=" O   ILE K 309 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'K' and resid 359 through 360
      removed outlier: 3.747A  pdb=" N   ILE K 359 " --> pdb=" O   TYR K 395 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   TYR K 395 " --> pdb=" O   ILE K 359 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AE3
    Processing sheet with id=AE4, first strand: chain 'K' and resid 374 through 375
      removed outlier: 3.516A  pdb=" N   PHE K 382 " --> pdb=" O   LYS K 421 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'K' and resid 423 through 424
    Processing sheet with id=AE6, first strand: chain 'M' and resid 10 through 12
      removed outlier: 3.684A  pdb=" N   THR M 124 " --> pdb=" O   GLU M  10 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   VAL M  93 " --> pdb=" O   LEU M  39 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   VAL M  37 " --> pdb=" O   TYR M  95 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   HIS M  35 " --> pdb=" O   VAL M  97 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   TYR M  33 " --> pdb=" O   GLY M  99 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   GLY M  49 " --> pdb=" O   TRP M  36 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   ARG M  38 " --> pdb=" O   TRP M  47 " (cutoff:3.500A)
      removed outlier: 4.849A  pdb=" N   TRP M  47 " --> pdb=" O   ARG M  38 " (cutoff:3.500A)
    Processing sheet with id=AE7, first strand: chain 'M' and resid 20 through 22
      removed outlier: 3.967A  pdb=" N   VAL M  20 " --> pdb=" O   MET M  81 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   THR M  78 " --> pdb=" O   ASP M  73 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   THR M  71 " --> pdb=" O   TYR M  80 " (cutoff:3.500A)
    Processing sheet with id=AE8, first strand: chain 'N' and resid 239 through 240
    Processing sheet with id=AE9, first strand: chain 'N' and resid 249 through 253
      removed outlier: 3.637A  pdb=" N   THR N 302 " --> pdb=" O   SER N 299 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   SER N 304 " --> pdb=" O   SER N 297 " (cutoff:3.500A)
    Processing sheet with id=AF1, first strand: chain 'N' and resid 274 through 281
      removed outlier: 5.314A  pdb=" N   ALA N 275 " --> pdb=" O   HIS N 271 " (cutoff:3.500A)
      removed outlier: 5.399A  pdb=" N   HIS N 271 " --> pdb=" O   ALA N 275 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   TRP N 267 " --> pdb=" O   LEU N 279 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   TYR N 281 " --> pdb=" O   VAL N 265 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   VAL N 265 " --> pdb=" O   TYR N 281 " (cutoff:3.500A)

    503 hydrogen bonds defined for protein.
    1305 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 6.35

  Time building geometry restraints manager: 6.78 seconds

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

  Histogram of bond lengths:
        1.21 -     1.35: 6264
        1.35 -     1.48: 5496
        1.48 -     1.61: 8526
        1.61 -     1.74: 3
        1.74 -     1.88: 174
  Bond restraints: 20463
  Sorted by residual:
  bond pdb=" CA  GLN K 258 "
       pdb=" C   GLN K 258 "
    ideal  model  delta    sigma   weight residual
    1.527  1.455  0.072 1.21e-02 6.83e+03 3.54e+01
  bond pdb=" C1  MAN R  11 "
       pdb=" C2  MAN R  11 "
    ideal  model  delta    sigma   weight residual
    1.526  1.631 -0.105 2.00e-02 2.50e+03 2.77e+01
  bond pdb=" C1  MAN R   7 "
       pdb=" C2  MAN R   7 "
    ideal  model  delta    sigma   weight residual
    1.526  1.615 -0.089 2.00e-02 2.50e+03 1.98e+01
  bond pdb=" C1  MAN J   8 "
       pdb=" C2  MAN J   8 "
    ideal  model  delta    sigma   weight residual
    1.526  1.614 -0.088 2.00e-02 2.50e+03 1.93e+01
  bond pdb=" CA  GLU K 370 "
       pdb=" C   GLU K 370 "
    ideal  model  delta    sigma   weight residual
    1.525  1.581 -0.056 1.35e-02 5.49e+03 1.74e+01
  ... (remaining 20458 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.13: 27043
        3.13 -     6.27: 739
        6.27 -     9.40: 58
        9.40 -    12.53: 7
       12.53 -    15.67: 2
  Bond angle restraints: 27849
  Sorted by residual:
  angle pdb=" C   ASN K  67 "
        pdb=" N   VAL K  68 "
        pdb=" CA  VAL K  68 "
      ideal   model   delta    sigma   weight residual
     121.70  136.00  -14.30 1.80e+00 3.09e-01 6.31e+01
  angle pdb=" C   ASN F  67 "
        pdb=" N   VAL F  68 "
        pdb=" CA  VAL F  68 "
      ideal   model   delta    sigma   weight residual
     121.70  133.76  -12.06 1.80e+00 3.09e-01 4.49e+01
  angle pdb=" C   SER D 326 "
        pdb=" N   ALA D 327 "
        pdb=" CA  ALA D 327 "
      ideal   model   delta    sigma   weight residual
     121.70  132.16  -10.46 1.80e+00 3.09e-01 3.38e+01
  angle pdb=" C   ASN A  67 "
        pdb=" N   VAL A  68 "
        pdb=" CA  VAL A  68 "
      ideal   model   delta    sigma   weight residual
     121.70  131.90  -10.20 1.80e+00 3.09e-01 3.21e+01
  angle pdb=" C   SER N 326 "
        pdb=" N   ALA N 327 "
        pdb=" CA  ALA N 327 "
      ideal   model   delta    sigma   weight residual
     121.70  131.82  -10.12 1.80e+00 3.09e-01 3.16e+01
  ... (remaining 27844 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.58: 12136
       22.58 -    45.15: 683
       45.15 -    67.73: 88
       67.73 -    90.31: 95
       90.31 -   112.88: 48
  Dihedral angle restraints: 13050
    sinusoidal: 5940
      harmonic: 7110
  Sorted by residual:
  dihedral pdb=" CA  CYS K 247 "
           pdb=" C   CYS K 247 "
           pdb=" N   THR K 248 "
           pdb=" CA  THR K 248 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -128.62  -51.38     0      5.00e+00 4.00e-02 1.06e+02
  dihedral pdb=" CB  CYS K 228 "
           pdb=" SG  CYS K 228 "
           pdb=" SG  CYS K 239 "
           pdb=" CB  CYS K 239 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    0.39  -86.39     1      1.00e+01 1.00e-02 9.00e+01
  dihedral pdb=" CB  CYS K 501 "
           pdb=" SG  CYS K 501 "
           pdb=" SG  CYS L 605 "
           pdb=" CB  CYS L 605 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    0.30  -86.30     1      1.00e+01 1.00e-02 8.98e+01
  ... (remaining 13047 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 2517
       0.061 -    0.122: 628
       0.122 -    0.183: 139
       0.183 -    0.244: 28
       0.244 -    0.305: 15
  Chirality restraints: 3327
  Sorted by residual:
  chirality pdb=" C1  MAN R  11 "
            pdb=" O2  MAN R  10 "
            pdb=" C2  MAN R  11 "
            pdb=" O5  MAN R  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.36    0.04 2.00e-02 2.50e+03 3.77e+00
  chirality pdb=" CA  PRO D 272 "
            pdb=" N   PRO D 272 "
            pdb=" C   PRO D 272 "
            pdb=" CB  PRO D 272 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.41    0.31 2.00e-01 2.50e+01 2.33e+00
  chirality pdb=" C5  BMA T   3 "
            pdb=" C4  BMA T   3 "
            pdb=" C6  BMA T   3 "
            pdb=" O5  BMA T   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.58    0.30 2.00e-01 2.50e+01 2.28e+00
  ... (remaining 3324 not shown)

  Planarity restraints: 3468
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS D 271 "   -0.098 5.00e-02 4.00e+02   1.51e-01 3.65e+01
        pdb=" N   PRO D 272 "    0.261 5.00e-02 4.00e+02
        pdb=" CA  PRO D 272 "   -0.089 5.00e-02 4.00e+02
        pdb=" CD  PRO D 272 "   -0.074 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP M  36 "   -0.003 2.00e-02 2.50e+03   2.22e-02 1.23e+01
        pdb=" CG  TRP M  36 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD1 TRP M  36 "   -0.000 2.00e-02 2.50e+03
        pdb=" CD2 TRP M  36 "    0.015 2.00e-02 2.50e+03
        pdb=" NE1 TRP M  36 "   -0.021 2.00e-02 2.50e+03
        pdb=" CE2 TRP M  36 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE3 TRP M  36 "    0.031 2.00e-02 2.50e+03
        pdb=" CZ2 TRP M  36 "    0.040 2.00e-02 2.50e+03
        pdb=" CZ3 TRP M  36 "   -0.038 2.00e-02 2.50e+03
        pdb=" CH2 TRP M  36 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP K 338 "    0.024 2.00e-02 2.50e+03   2.14e-02 1.15e+01
        pdb=" CG  TRP K 338 "   -0.058 2.00e-02 2.50e+03
        pdb=" CD1 TRP K 338 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP K 338 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP K 338 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP K 338 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP K 338 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP K 338 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP K 338 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP K 338 "    0.003 2.00e-02 2.50e+03
  ... (remaining 3465 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 216
        2.58 -     3.16: 16854
        3.16 -     3.74: 28691
        3.74 -     4.32: 39941
        4.32 -     4.90: 65398
  Nonbonded interactions: 151100
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 163 "
            pdb=" OE1 GLU A 164 "
     model   vdw
     2.002 3.040
  nonbonded pdb=" OG  SER I 299 "
            pdb=" O   THR I 302 "
     model   vdw
     2.042 3.040
  nonbonded pdb=" OG1 THR F 163 "
            pdb=" OE1 GLU F 164 "
     model   vdw
     2.047 3.040
  nonbonded pdb=" O   VAL F  36 "
            pdb=" OG1 THR G 606 "
     model   vdw
     2.060 3.040
  nonbonded pdb=" OG1 THR F 161 "
            pdb=" O   LYS F 170 "
     model   vdw
     2.077 3.040
  ... (remaining 151095 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'F'
  selection = chain 'K'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'G'
  selection = chain 'L'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'H'
  selection = chain 'M'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'I'
  selection = chain 'N'
}
ncs_group {
  reference = chain 'J'
  selection = chain 'V'
}
ncs_group {
  reference = chain 'O'
  selection = chain 'P'
  selection = chain 'S'
  selection = chain 'T'
}
ncs_group {
  reference = chain 'Q'
  selection = chain 'U'
}
ncs_group {
  reference = chain 'W'
  selection = chain 'X'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.380
  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:          0.760
  Check model and map are aligned:         0.130
  Set scattering table:                    0.170
  Process input model:                     46.340
  Find NCS groups from input model:        0.680
  Set up NCS constraints:                  0.120
  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:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   53.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7002
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   0.105  20463  Z= 0.522
  Angle     :  1.182  15.665  27849  Z= 0.631
  Chirality :  0.061   0.305   3327
  Planarity :  0.008   0.151   3456
  Dihedral  : 17.265 112.884   8367
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  8.66 %
    Favored  : 90.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.95 %
    Twisted General : 0.21 %

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: -3.16 (0.15), residues: 2448
  helix: -2.10 (0.26), residues: 298
  sheet: -1.75 (0.20), residues: 590
  loop : -2.34 (0.14), residues: 1560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.003   TRP K 338 
 HIS   0.028   0.004   HIS N 270 
 PHE   0.029   0.004   PHE F 468 
 TYR   0.034   0.003   TYR A 486 
 ARG   0.057   0.002   ARG L 542 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  748 residues out of total 2142 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 748
  time to evaluate  : 2.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 GLN cc_start: 0.7733 (tt0) cc_final: 0.7447 (tt0)
REVERT: A  154 MET cc_start: 0.8638 (pmm) cc_final: 0.8139 (pmm)
REVERT: B  530 MET cc_start: 0.8283 (mmm) cc_final: 0.7958 (mpp)
REVERT: C  101 TRP cc_start: 0.7573 (t60) cc_final: 0.7113 (t60)
REVERT: D  282 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7288 (mt-10)
REVERT: D  301 ASN cc_start: 0.8315 (m-40) cc_final: 0.7992 (t0)
REVERT: D  326 SER cc_start: 0.7837 (m) cc_final: 0.6917 (p)
REVERT: F  104 MET cc_start: 0.8814 (ttt) cc_final: 0.8517 (ttt)
REVERT: F  161 THR cc_start: 0.6053 (p) cc_final: 0.5741 (p)
REVERT: F  268 LYS cc_start: 0.8109 (ptmt) cc_final: 0.7851 (mttm)
REVERT: F  318 TYR cc_start: 0.8362 (m-80) cc_final: 0.7829 (m-10)
REVERT: F  427 TRP cc_start: 0.7686 (m-90) cc_final: 0.7459 (m-90)
REVERT: G  610 TRP cc_start: 0.6804 (t-100) cc_final: 0.6081 (t-100)
REVERT: H   84 ARG cc_start: 0.7175 (mpp80) cc_final: 0.6712 (mtm110)
REVERT: I  305 LEU cc_start: 0.5430 (mp) cc_final: 0.4661 (tt)
REVERT: I  326 SER cc_start: 0.7351 (m) cc_final: 0.6950 (p)
REVERT: K   42 VAL cc_start: 0.9196 (t) cc_final: 0.8925 (p)
REVERT: K   84 LEU cc_start: 0.7241 (tp) cc_final: 0.7010 (tt)
REVERT: K   96 TRP cc_start: 0.7900 (m-90) cc_final: 0.7103 (m-90)
REVERT: L  603 ILE cc_start: 0.9049 (mm) cc_final: 0.8832 (tt)
REVERT: L  645 LEU cc_start: 0.8330 (mt) cc_final: 0.8019 (tp)
REVERT: L  647 GLU cc_start: 0.6995 (pp20) cc_final: 0.6778 (pp20)
REVERT: M    3 GLN cc_start: 0.7409 (tm-30) cc_final: 0.7004 (tm-30)
REVERT: M   38 ARG cc_start: 0.7475 (ttp-170) cc_final: 0.7058 (ttp80)
REVERT: M  103 SER cc_start: 0.8523 (t) cc_final: 0.8222 (p)
REVERT: N  259 VAL cc_start: 0.8093 (t) cc_final: 0.7117 (p)
REVERT: N  267 TRP cc_start: 0.7822 (m100) cc_final: 0.7586 (m100)
REVERT: N  279 LEU cc_start: 0.8761 (pp) cc_final: 0.8504 (pp)
REVERT: N  301 ASN cc_start: 0.7542 (m-40) cc_final: 0.6853 (t0)
REVERT: N  336 LYS cc_start: 0.8700 (tptt) cc_final: 0.8429 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 748
  average time/residue: 0.3314
  time to fit residues: 366.0850
Evaluate side-chains
  371 residues out of total 2142 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 371
  time to evaluate  : 2.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 243
   random chunks:
   chunk 205 optimal weight:    0.9990
   chunk 184 optimal weight:    1.9990
   chunk 102 optimal weight:    0.7980
   chunk 62 optimal weight:    0.7980
   chunk 124 optimal weight:    0.9980
   chunk 98 optimal weight:    0.0070
   chunk 190 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 115 optimal weight:    0.7980
   chunk 141 optimal weight:    0.9990
   chunk 220 optimal weight:    6.9990
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
** A  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 577 GLN
B 653 GLN
D 271 HIS
** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 287 HIS
F 300 ASN
F 330 HIS
G 577 GLN
G 630 GLN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 116 HIS
L 651 ASN
L 653 GLN
** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.3542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  20463  Z= 0.252
  Angle     :  0.820  12.949  27849  Z= 0.415
  Chirality :  0.050   0.267   3327
  Planarity :  0.006   0.097   3456
  Dihedral  : 13.044  84.161   3954
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.05 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 13.63 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -2.68 (0.16), residues: 2448
  helix: -1.30 (0.28), residues: 312
  sheet: -1.40 (0.19), residues: 657
  loop : -2.14 (0.15), residues: 1479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP K 479 
 HIS   0.008   0.002   HIS F 249 
 PHE   0.033   0.002   PHE C 114 
 TYR   0.019   0.002   TYR K 217 
 ARG   0.005   0.001   ARG H  38 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  489 residues out of total 2142 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 65
    poor density    : 424
  time to evaluate  : 2.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ASP cc_start: 0.6481 (t0) cc_final: 0.5969 (p0)
REVERT: A   83 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7419 (tm-30)
REVERT: A  128 THR cc_start: 0.8843 (p) cc_final: 0.8601 (t)
REVERT: A  184 LEU cc_start: 0.8496 (tt) cc_final: 0.6847 (tp)
REVERT: B  530 MET cc_start: 0.8936 (mmm) cc_final: 0.8235 (mpp)
REVERT: B  643 TYR cc_start: 0.8623 (m-10) cc_final: 0.8423 (m-80)
REVERT: B  656 ASN cc_start: 0.8032 (t0) cc_final: 0.7774 (t0)
REVERT: C  101 TRP cc_start: 0.8059 (t60) cc_final: 0.7390 (t60)
REVERT: D  282 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7431 (mt-10)
REVERT: D  301 ASN cc_start: 0.8560 (m-40) cc_final: 0.8126 (m-40)
REVERT: F  104 MET cc_start: 0.9055 (ttt) cc_final: 0.8641 (ttm)
REVERT: F  268 LYS cc_start: 0.8315 (ptmt) cc_final: 0.7869 (mttm)
REVERT: F  318 TYR cc_start: 0.7876 (m-80) cc_final: 0.7551 (m-10)
REVERT: F  387 THR cc_start: 0.8058 (p) cc_final: 0.7499 (t)
REVERT: F  426 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7530 (ptp)
REVERT: G  630 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8307 (mp10)
REVERT: H   39 LEU cc_start: 0.8345 (mt) cc_final: 0.8094 (mt)
REVERT: H   84 ARG cc_start: 0.7353 (mpp80) cc_final: 0.7008 (mtm180)
REVERT: I  305 LEU cc_start: 0.5666 (mp) cc_final: 0.4687 (tt)
REVERT: K   96 TRP cc_start: 0.7893 (m-90) cc_final: 0.7175 (m-90)
REVERT: L  646 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.9009 (mm)
REVERT: M  103 SER cc_start: 0.8756 (t) cc_final: 0.8544 (p)
REVERT: N  301 ASN cc_start: 0.7636 (m-40) cc_final: 0.7056 (t0)
  outliers start: 65
  outliers final: 36
  residues processed: 459
  average time/residue: 0.2979
  time to fit residues: 211.3266
Evaluate side-chains
  369 residues out of total 2142 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 330
  time to evaluate  : 2.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain B residue  592 LEU
Chi-restraints excluded: chain B residue  641 ILE
Chi-restraints excluded: chain D residue  248 ILE
Chi-restraints excluded: chain D residue  306 THR
Chi-restraints excluded: chain D residue  307 ILE
Chi-restraints excluded: chain F residue   84 LEU
Chi-restraints excluded: chain F residue  182 VAL
Chi-restraints excluded: chain F residue  201 CYS
Chi-restraints excluded: chain F residue  288 LEU
Chi-restraints excluded: chain F residue  377 ASN
Chi-restraints excluded: chain F residue  426 MET
Chi-restraints excluded: chain G residue  529 THR
Chi-restraints excluded: chain G residue  580 VAL
Chi-restraints excluded: chain G residue  615 SER
Chi-restraints excluded: chain G residue  623 TRP
Chi-restraints excluded: chain G residue  624 ASP
Chi-restraints excluded: chain G residue  630 GLN
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain I residue  253 THR
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   72 HIS
Chi-restraints excluded: chain K residue  128 THR
Chi-restraints excluded: chain K residue  182 VAL
Chi-restraints excluded: chain K residue  215 ILE
Chi-restraints excluded: chain K residue  249 HIS
Chi-restraints excluded: chain K residue  445 CYS
Chi-restraints excluded: chain L residue  580 VAL
Chi-restraints excluded: chain L residue  608 VAL
Chi-restraints excluded: chain L residue  646 LEU
Chi-restraints excluded: chain M residue  115 ASP
Chi-restraints excluded: chain N residue  265 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 243
   random chunks:
   chunk 122 optimal weight:    5.9990
   chunk 68 optimal weight:    2.9990
   chunk 183 optimal weight:    0.7980
   chunk 150 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 221 optimal weight:    8.9990
   chunk 238 optimal weight:    7.9990
   chunk 196 optimal weight:    0.9990
   chunk 219 optimal weight:    7.9990
   chunk 75 optimal weight:    3.9990
   chunk 177 optimal weight:    3.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 289 HIS
A 300 ASN
C  63 ASN
D 246 GLN
** F  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 105 HIS
F 187 ASN
F 362 ASN
G 591 GLN
** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  62 GLN
H  63 ASN
** K  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 374 HIS
** L 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 651 ASN
M  63 ASN
** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.5088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.089  20463  Z= 0.400
  Angle     :  0.890  14.163  27849  Z= 0.447
  Chirality :  0.052   0.255   3327
  Planarity :  0.006   0.079   3456
  Dihedral  :  9.712  57.765   3954
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  7.07 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 15.97 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

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: -2.54 (0.16), residues: 2448
  helix: -0.84 (0.29), residues: 304
  sheet: -1.32 (0.18), residues: 683
  loop : -2.12 (0.15), residues: 1461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP D 267 
 HIS   0.012   0.002   HIS A 330 
 PHE   0.042   0.003   PHE C 114 
 TYR   0.031   0.002   TYR H  33 
 ARG   0.010   0.001   ARG G 617 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  486 residues out of total 2142 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 113
    poor density    : 373
  time to evaluate  : 2.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LYS cc_start: 0.8923 (mtmt) cc_final: 0.8677 (mtpt)
REVERT: A   57 ASP cc_start: 0.6853 (t0) cc_final: 0.6611 (m-30)
REVERT: B  530 MET cc_start: 0.9189 (mmm) cc_final: 0.8412 (mpp)
REVERT: B  542 ARG cc_start: 0.7791 (ttp80) cc_final: 0.7563 (ttt-90)
REVERT: B  632 ASP cc_start: 0.8662 (t0) cc_final: 0.8403 (t70)
REVERT: B  643 TYR cc_start: 0.8775 (m-10) cc_final: 0.8572 (m-80)
REVERT: B  656 ASN cc_start: 0.8178 (t0) cc_final: 0.7964 (t0)
REVERT: C   60 GLN cc_start: 0.8190 (pm20) cc_final: 0.7465 (mm-40)
REVERT: D  272 PRO cc_start: 0.7686 (OUTLIER) cc_final: 0.7223 (Cg_endo)
REVERT: D  280 ILE cc_start: 0.7572 (mm) cc_final: 0.7286 (mm)
REVERT: D  282 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7543 (mt-10)
REVERT: D  314 ASP cc_start: 0.7685 (m-30) cc_final: 0.7313 (m-30)
REVERT: F  104 MET cc_start: 0.9123 (ttt) cc_final: 0.8757 (ttt)
REVERT: F  268 LYS cc_start: 0.8503 (ptmt) cc_final: 0.8054 (mttm)
REVERT: G  630 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8126 (pm20)
REVERT: H   13 ASN cc_start: 0.6898 (p0) cc_final: 0.6618 (p0)
REVERT: H   39 LEU cc_start: 0.8189 (mt) cc_final: 0.7946 (mt)
REVERT: I  248 ILE cc_start: 0.6595 (OUTLIER) cc_final: 0.6018 (mm)
REVERT: I  305 LEU cc_start: 0.5726 (mp) cc_final: 0.4646 (tt)
REVERT: K  369 MET cc_start: 0.6861 (tpp) cc_final: 0.6453 (ttt)
REVERT: K  381 GLU cc_start: 0.7664 (tp30) cc_final: 0.7435 (tp30)
REVERT: L  630 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7707 (mp10)
REVERT: L  646 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8961 (mm)
REVERT: M   10 GLU cc_start: 0.7194 (pm20) cc_final: 0.6573 (pp20)
REVERT: M   47 TRP cc_start: 0.7014 (t60) cc_final: 0.6248 (t60)
REVERT: N  301 ASN cc_start: 0.8097 (m-40) cc_final: 0.7583 (t0)
  outliers start: 113
  outliers final: 70
  residues processed: 442
  average time/residue: 0.2947
  time to fit residues: 203.2695
Evaluate side-chains
  372 residues out of total 2142 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 75
    poor density    : 297
  time to evaluate  : 2.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  388 SER
Chi-restraints excluded: chain A residue  446 ARG
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain B residue  537 LEU
Chi-restraints excluded: chain B residue  641 ILE
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   63 ASN
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain D residue  247 SER
Chi-restraints excluded: chain D residue  248 ILE
Chi-restraints excluded: chain D residue  250 ILE
Chi-restraints excluded: chain D residue  272 PRO
Chi-restraints excluded: chain D residue  306 THR
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue  111 LEU
Chi-restraints excluded: chain F residue  120 VAL
Chi-restraints excluded: chain F residue  182 VAL
Chi-restraints excluded: chain F residue  297 THR
Chi-restraints excluded: chain F residue  362 ASN
Chi-restraints excluded: chain F residue  377 ASN
Chi-restraints excluded: chain F residue  446 ARG
Chi-restraints excluded: chain F residue  450 THR
Chi-restraints excluded: chain G residue  529 THR
Chi-restraints excluded: chain G residue  583 VAL
Chi-restraints excluded: chain G residue  608 VAL
Chi-restraints excluded: chain G residue  615 SER
Chi-restraints excluded: chain G residue  623 TRP
Chi-restraints excluded: chain G residue  624 ASP
Chi-restraints excluded: chain G residue  626 MET
Chi-restraints excluded: chain G residue  630 GLN
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   89 ASP
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue   98 THR
Chi-restraints excluded: chain I residue  248 ILE
Chi-restraints excluded: chain I residue  288 SER
Chi-restraints excluded: chain I residue  295 SER
Chi-restraints excluded: chain I residue  326 SER
Chi-restraints excluded: chain I residue  340 LEU
Chi-restraints excluded: chain K residue   42 VAL
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue  113 ASP
Chi-restraints excluded: chain K residue  182 VAL
Chi-restraints excluded: chain K residue  202 THR
Chi-restraints excluded: chain K residue  215 ILE
Chi-restraints excluded: chain K residue  271 VAL
Chi-restraints excluded: chain K residue  434 MET
Chi-restraints excluded: chain K residue  445 CYS
Chi-restraints excluded: chain K residue  450 THR
Chi-restraints excluded: chain L residue  580 VAL
Chi-restraints excluded: chain L residue  592 LEU
Chi-restraints excluded: chain L residue  603 ILE
Chi-restraints excluded: chain L residue  608 VAL
Chi-restraints excluded: chain L residue  615 SER
Chi-restraints excluded: chain L residue  630 GLN
Chi-restraints excluded: chain L residue  646 LEU
Chi-restraints excluded: chain M residue   13 ASN
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain M residue  115 ASP
Chi-restraints excluded: chain N residue  259 VAL
Chi-restraints excluded: chain N residue  265 VAL
Chi-restraints excluded: chain N residue  314 ASP
Chi-restraints excluded: chain N residue  339 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 243
   random chunks:
   chunk 218 optimal weight:    0.9980
   chunk 166 optimal weight:   10.0000
   chunk 114 optimal weight:    0.6980
   chunk 24 optimal weight:    4.9990
   chunk 105 optimal weight:    4.9990
   chunk 148 optimal weight:    0.8980
   chunk 221 optimal weight:    9.9990
   chunk 234 optimal weight:    5.9990
   chunk 115 optimal weight:    0.6980
   chunk 210 optimal weight:    3.9990
   chunk 63 optimal weight:    0.0070
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
C  63 ASN
D 246 GLN
** F  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 203 GLN
F 362 ASN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.5405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  20463  Z= 0.208
  Angle     :  0.744  15.408  27849  Z= 0.373
  Chirality :  0.048   0.228   3327
  Planarity :  0.005   0.075   3456
  Dihedral  :  8.592  59.269   3954
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.76 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 19.61 %
    Favored  : 76.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.38 %
    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: -2.41 (0.16), residues: 2448
  helix: -0.75 (0.29), residues: 327
  sheet: -1.03 (0.19), residues: 638
  loop : -2.16 (0.14), residues: 1483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP M  36 
 HIS   0.006   0.001   HIS K  72 
 PHE   0.017   0.002   PHE C 114 
 TYR   0.024   0.001   TYR N 278 
 ARG   0.007   0.001   ARG A  59 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  444 residues out of total 2142 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 94
    poor density    : 350
  time to evaluate  : 2.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 LYS cc_start: 0.8654 (mmmt) cc_final: 0.8427 (mmtp)
REVERT: A  280 ASN cc_start: 0.8459 (m110) cc_final: 0.8093 (m-40)
REVERT: B  530 MET cc_start: 0.9107 (mmm) cc_final: 0.8457 (mpp)
REVERT: B  542 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7660 (ttt-90)
REVERT: B  632 ASP cc_start: 0.8592 (t0) cc_final: 0.8367 (t70)
REVERT: B  656 ASN cc_start: 0.8120 (t0) cc_final: 0.7872 (t0)
REVERT: C   60 GLN cc_start: 0.8137 (pm20) cc_final: 0.7483 (mm-40)
REVERT: D  272 PRO cc_start: 0.7658 (OUTLIER) cc_final: 0.7241 (Cg_endo)
REVERT: D  282 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7454 (mt-10)
REVERT: D  314 ASP cc_start: 0.7654 (m-30) cc_final: 0.7292 (m-30)
REVERT: F  104 MET cc_start: 0.9022 (ttt) cc_final: 0.8650 (ttt)
REVERT: F  268 LYS cc_start: 0.8504 (ptmt) cc_final: 0.8035 (mttm)
REVERT: G  634 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7010 (mt-10)
REVERT: H   39 LEU cc_start: 0.8193 (mt) cc_final: 0.7952 (mt)
REVERT: I  268 TYR cc_start: 0.8858 (m-80) cc_final: 0.8574 (m-80)
REVERT: I  305 LEU cc_start: 0.5597 (mp) cc_final: 0.4604 (tt)
REVERT: K  479 TRP cc_start: 0.8505 (m-10) cc_final: 0.8023 (m-90)
REVERT: L  529 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8301 (t)
REVERT: M   10 GLU cc_start: 0.7124 (pm20) cc_final: 0.6630 (pp20)
REVERT: M   38 ARG cc_start: 0.7324 (ttm110) cc_final: 0.6758 (mtp85)
REVERT: M   47 TRP cc_start: 0.6753 (t60) cc_final: 0.6366 (t60)
REVERT: M   59 ASN cc_start: 0.8576 (t0) cc_final: 0.7982 (t0)
REVERT: M   72 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6475 (ptt-90)
REVERT: M   94 TYR cc_start: 0.7544 (m-80) cc_final: 0.6899 (m-10)
REVERT: M  104 ASP cc_start: 0.8458 (t0) cc_final: 0.8227 (t70)
REVERT: N  301 ASN cc_start: 0.8052 (m-40) cc_final: 0.7585 (t0)
  outliers start: 94
  outliers final: 64
  residues processed: 409
  average time/residue: 0.2920
  time to fit residues: 187.5183
Evaluate side-chains
  374 residues out of total 2142 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 67
    poor density    : 307
  time to evaluate  : 2.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  377 ASN
Chi-restraints excluded: chain A residue  446 ARG
Chi-restraints excluded: chain B residue  641 ILE
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain D residue  247 SER
Chi-restraints excluded: chain D residue  248 ILE
Chi-restraints excluded: chain D residue  259 VAL
Chi-restraints excluded: chain D residue  272 PRO
Chi-restraints excluded: chain D residue  306 THR
Chi-restraints excluded: chain D residue  340 LEU
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue  169 GLU
Chi-restraints excluded: chain F residue  182 VAL
Chi-restraints excluded: chain F residue  202 THR
Chi-restraints excluded: chain F residue  217 TYR
Chi-restraints excluded: chain F residue  271 VAL
Chi-restraints excluded: chain F residue  297 THR
Chi-restraints excluded: chain F residue  362 ASN
Chi-restraints excluded: chain F residue  377 ASN
Chi-restraints excluded: chain F residue  433 CYS
Chi-restraints excluded: chain F residue  446 ARG
Chi-restraints excluded: chain F residue  450 THR
Chi-restraints excluded: chain G residue  595 ILE
Chi-restraints excluded: chain G residue  615 SER
Chi-restraints excluded: chain G residue  624 ASP
Chi-restraints excluded: chain G residue  647 GLU
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   76 ILE
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain I residue  248 ILE
Chi-restraints excluded: chain I residue  288 SER
Chi-restraints excluded: chain I residue  295 SER
Chi-restraints excluded: chain I residue  326 SER
Chi-restraints excluded: chain I residue  340 LEU
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   85 VAL
Chi-restraints excluded: chain K residue  182 VAL
Chi-restraints excluded: chain K residue  202 THR
Chi-restraints excluded: chain K residue  215 ILE
Chi-restraints excluded: chain K residue  218 CYS
Chi-restraints excluded: chain K residue  249 HIS
Chi-restraints excluded: chain K residue  288 LEU
Chi-restraints excluded: chain K residue  289 HIS
Chi-restraints excluded: chain K residue  390 LEU
Chi-restraints excluded: chain K residue  434 MET
Chi-restraints excluded: chain K residue  445 CYS
Chi-restraints excluded: chain K residue  450 THR
Chi-restraints excluded: chain L residue  529 THR
Chi-restraints excluded: chain L residue  580 VAL
Chi-restraints excluded: chain L residue  581 LEU
Chi-restraints excluded: chain L residue  608 VAL
Chi-restraints excluded: chain M residue   13 ASN
Chi-restraints excluded: chain M residue   39 LEU
Chi-restraints excluded: chain M residue   72 ARG
Chi-restraints excluded: chain N residue  265 VAL
Chi-restraints excluded: chain N residue  339 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 243
   random chunks:
   chunk 195 optimal weight:    1.9990
   chunk 133 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 174 optimal weight:    3.9990
   chunk 96 optimal weight:    0.5980
   chunk 200 optimal weight:    3.9990
   chunk 162 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 119 optimal weight:    0.0970
   chunk 210 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0270
   overall best weight:    0.7440

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

Flipped N/Q/H residues before XYZ refinement:
** A  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 280 ASN
D 246 GLN
** F  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN
K 246 GLN
** L 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.5682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  20463  Z= 0.212
  Angle     :  0.724  12.841  27849  Z= 0.361
  Chirality :  0.047   0.246   3327
  Planarity :  0.005   0.074   3456
  Dihedral  :  7.958  58.843   3954
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.45 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 20.68 %
    Favored  : 75.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -2.32 (0.16), residues: 2448
  helix: -0.34 (0.30), residues: 320
  sheet: -1.01 (0.18), residues: 680
  loop : -2.17 (0.15), residues: 1448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  96 
 HIS   0.005   0.001   HIS K  72 
 PHE   0.024   0.001   PHE M  64 
 TYR   0.023   0.001   TYR N 278 
 ARG   0.003   0.000   ARG I 293 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  418 residues out of total 2142 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 90
    poor density    : 328
  time to evaluate  : 2.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LYS cc_start: 0.8723 (mtmt) cc_final: 0.8519 (mtpt)
REVERT: A  280 ASN cc_start: 0.8520 (m-40) cc_final: 0.8171 (m-40)
REVERT: B  530 MET cc_start: 0.9096 (mmm) cc_final: 0.8300 (mpp)
REVERT: B  542 ARG cc_start: 0.8007 (ttp80) cc_final: 0.7656 (ttt-90)
REVERT: B  592 LEU cc_start: 0.8490 (mm) cc_final: 0.8264 (mt)
REVERT: B  639 THR cc_start: 0.8419 (p) cc_final: 0.8067 (t)
REVERT: B  656 ASN cc_start: 0.8200 (t0) cc_final: 0.7908 (t0)
REVERT: C   60 GLN cc_start: 0.8132 (pm20) cc_final: 0.7507 (mm-40)
REVERT: D  272 PRO cc_start: 0.7737 (OUTLIER) cc_final: 0.7310 (Cg_endo)
REVERT: D  282 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7472 (mt-10)
REVERT: D  301 ASN cc_start: 0.8809 (m-40) cc_final: 0.8556 (t0)
REVERT: D  314 ASP cc_start: 0.7588 (m-30) cc_final: 0.7232 (m-30)
REVERT: F  104 MET cc_start: 0.8996 (ttt) cc_final: 0.8663 (ttt)
REVERT: F  268 LYS cc_start: 0.8534 (ptmt) cc_final: 0.8114 (mmtm)
REVERT: H    3 GLN cc_start: 0.8414 (pm20) cc_final: 0.8116 (pm20)
REVERT: H   39 LEU cc_start: 0.8303 (mt) cc_final: 0.7990 (mt)
REVERT: I  246 GLN cc_start: 0.9171 (tt0) cc_final: 0.8936 (pp30)
REVERT: I  268 TYR cc_start: 0.8831 (m-80) cc_final: 0.8529 (m-80)
REVERT: I  305 LEU cc_start: 0.5705 (mp) cc_final: 0.4725 (tt)
REVERT: K   49 LYS cc_start: 0.8492 (tttm) cc_final: 0.7946 (mtpt)
REVERT: K  104 MET cc_start: 0.8494 (ttt) cc_final: 0.8213 (ttt)
REVERT: K  479 TRP cc_start: 0.8490 (m-10) cc_final: 0.8044 (m-90)
REVERT: L  529 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8317 (t)
REVERT: L  623 TRP cc_start: 0.8149 (OUTLIER) cc_final: 0.7609 (m-90)
REVERT: L  633 LYS cc_start: 0.9246 (pptt) cc_final: 0.8920 (pptt)
REVERT: M   10 GLU cc_start: 0.7110 (pm20) cc_final: 0.6775 (pp20)
REVERT: M   47 TRP cc_start: 0.6797 (t60) cc_final: 0.6468 (t60)
REVERT: M   59 ASN cc_start: 0.8608 (t0) cc_final: 0.7993 (t0)
REVERT: M  102 ILE cc_start: 0.8212 (mt) cc_final: 0.7682 (pt)
REVERT: N  285 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7287 (mtmm)
REVERT: N  301 ASN cc_start: 0.8100 (m-40) cc_final: 0.7654 (t0)
  outliers start: 90
  outliers final: 71
  residues processed: 389
  average time/residue: 0.2813
  time to fit residues: 173.4544
Evaluate side-chains
  376 residues out of total 2142 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 75
    poor density    : 301
  time to evaluate  : 2.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  446 ARG
Chi-restraints excluded: chain B residue  641 ILE
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   70 MET
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain D residue  246 GLN
Chi-restraints excluded: chain D residue  248 ILE
Chi-restraints excluded: chain D residue  259 VAL
Chi-restraints excluded: chain D residue  272 PRO
Chi-restraints excluded: chain D residue  306 THR
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue  169 GLU
Chi-restraints excluded: chain F residue  182 VAL
Chi-restraints excluded: chain F residue  202 THR
Chi-restraints excluded: chain F residue  217 TYR
Chi-restraints excluded: chain F residue  271 VAL
Chi-restraints excluded: chain F residue  292 VAL
Chi-restraints excluded: chain F residue  297 THR
Chi-restraints excluded: chain F residue  377 ASN
Chi-restraints excluded: chain F residue  394 THR
Chi-restraints excluded: chain F residue  433 CYS
Chi-restraints excluded: chain F residue  450 THR
Chi-restraints excluded: chain G residue  583 VAL
Chi-restraints excluded: chain G residue  595 ILE
Chi-restraints excluded: chain G residue  615 SER
Chi-restraints excluded: chain G residue  624 ASP
Chi-restraints excluded: chain G residue  647 GLU
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   76 ILE
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain I residue  248 ILE
Chi-restraints excluded: chain I residue  253 THR
Chi-restraints excluded: chain I residue  259 VAL
Chi-restraints excluded: chain I residue  288 SER
Chi-restraints excluded: chain I residue  295 SER
Chi-restraints excluded: chain I residue  340 LEU
Chi-restraints excluded: chain K residue   42 VAL
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   68 VAL
Chi-restraints excluded: chain K residue  182 VAL
Chi-restraints excluded: chain K residue  202 THR
Chi-restraints excluded: chain K residue  215 ILE
Chi-restraints excluded: chain K residue  218 CYS
Chi-restraints excluded: chain K residue  249 HIS
Chi-restraints excluded: chain K residue  288 LEU
Chi-restraints excluded: chain K residue  289 HIS
Chi-restraints excluded: chain K residue  292 VAL
Chi-restraints excluded: chain K residue  434 MET
Chi-restraints excluded: chain K residue  445 CYS
Chi-restraints excluded: chain K residue  450 THR
Chi-restraints excluded: chain K residue  501 CYS
Chi-restraints excluded: chain L residue  529 THR
Chi-restraints excluded: chain L residue  580 VAL
Chi-restraints excluded: chain L residue  581 LEU
Chi-restraints excluded: chain L residue  587 LEU
Chi-restraints excluded: chain L residue  592 LEU
Chi-restraints excluded: chain L residue  608 VAL
Chi-restraints excluded: chain L residue  623 TRP
Chi-restraints excluded: chain L residue  630 GLN
Chi-restraints excluded: chain M residue   39 LEU
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain N residue  265 VAL
Chi-restraints excluded: chain N residue  285 LYS
Chi-restraints excluded: chain N residue  339 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 243
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 211 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0070
   chunk 137 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 235 optimal weight:    4.9990
   chunk 195 optimal weight:    0.9990
   chunk 108 optimal weight:    0.1980
   chunk 19 optimal weight:    2.9990
   chunk 77 optimal weight:   20.0000
   chunk 123 optimal weight:    4.9990
   overall best weight:    0.6000

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

Flipped N/Q/H residues before XYZ refinement:
A 339 ASN
C   3 GLN
C  62 GLN
** F  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 630 GLN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN
** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 311 GLN
** K  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.5908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  20463  Z= 0.197
  Angle     :  0.705  12.963  27849  Z= 0.352
  Chirality :  0.046   0.232   3327
  Planarity :  0.005   0.072   3456
  Dihedral  :  7.551  59.290   3954
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.00 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 20.77 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

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: -2.17 (0.16), residues: 2448
  helix: -0.12 (0.31), residues: 318
  sheet: -0.72 (0.19), residues: 659
  loop : -2.19 (0.14), residues: 1471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP H  47 
 HIS   0.005   0.001   HIS K  72 
 PHE   0.024   0.001   PHE M  64 
 TYR   0.021   0.001   TYR N 278 
 ARG   0.007   0.000   ARG M  38 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  441 residues out of total 2142 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 107
    poor density    : 334
  time to evaluate  : 2.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  280 ASN cc_start: 0.8573 (m-40) cc_final: 0.8296 (m-40)
REVERT: A  439 ILE cc_start: 0.9666 (tp) cc_final: 0.9363 (mm)
REVERT: B  529 THR cc_start: 0.8983 (p) cc_final: 0.8691 (t)
REVERT: B  530 MET cc_start: 0.9081 (mmm) cc_final: 0.8284 (mpp)
REVERT: B  542 ARG cc_start: 0.7993 (ttp80) cc_final: 0.7678 (ttt-90)
REVERT: B  656 ASN cc_start: 0.8261 (t0) cc_final: 0.7958 (t0)
REVERT: C   60 GLN cc_start: 0.8088 (pm20) cc_final: 0.7441 (mm-40)
REVERT: D  272 PRO cc_start: 0.7680 (OUTLIER) cc_final: 0.7249 (Cg_endo)
REVERT: D  282 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7534 (mt-10)
REVERT: D  301 ASN cc_start: 0.8794 (m-40) cc_final: 0.8574 (t0)
REVERT: D  314 ASP cc_start: 0.7642 (m-30) cc_final: 0.7432 (m-30)
REVERT: F  104 MET cc_start: 0.8983 (ttt) cc_final: 0.8657 (ttt)
REVERT: F  268 LYS cc_start: 0.8506 (ptmt) cc_final: 0.8021 (mttm)
REVERT: F  423 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8674 (mp)
REVERT: F  446 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7777 (ttm110)
REVERT: H   39 LEU cc_start: 0.8317 (mt) cc_final: 0.8001 (mt)
REVERT: I  246 GLN cc_start: 0.9186 (tt0) cc_final: 0.8968 (pp30)
REVERT: K   49 LYS cc_start: 0.8440 (tttm) cc_final: 0.7902 (mtmt)
REVERT: K  104 MET cc_start: 0.8501 (ttt) cc_final: 0.8144 (ttt)
REVERT: K  128 THR cc_start: 0.9267 (OUTLIER) cc_final: 0.8918 (p)
REVERT: K  280 ASN cc_start: 0.7959 (m-40) cc_final: 0.7680 (t0)
REVERT: K  479 TRP cc_start: 0.8416 (m-10) cc_final: 0.8111 (m-90)
REVERT: L  529 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8421 (t)
REVERT: L  616 ASN cc_start: 0.7261 (t0) cc_final: 0.7051 (t0)
REVERT: L  623 TRP cc_start: 0.8154 (OUTLIER) cc_final: 0.7693 (m-90)
REVERT: L  633 LYS cc_start: 0.9303 (pptt) cc_final: 0.9051 (pptt)
REVERT: M    6 GLN cc_start: 0.7582 (pt0) cc_final: 0.6974 (pt0)
REVERT: M   10 GLU cc_start: 0.7065 (pm20) cc_final: 0.6762 (pp20)
REVERT: M   59 ASN cc_start: 0.8607 (t0) cc_final: 0.8048 (t0)
REVERT: M   81 MET cc_start: 0.8662 (mmm) cc_final: 0.8400 (mmm)
REVERT: M  102 ILE cc_start: 0.8199 (mt) cc_final: 0.7715 (pt)
REVERT: N  301 ASN cc_start: 0.8174 (m-40) cc_final: 0.7671 (t0)
  outliers start: 107
  outliers final: 71
  residues processed: 408
  average time/residue: 0.2795
  time to fit residues: 181.8988
Evaluate side-chains
  388 residues out of total 2142 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 77
    poor density    : 311
  time to evaluate  : 2.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  426 MET
Chi-restraints excluded: chain A residue  446 ARG
Chi-restraints excluded: chain B residue  641 ILE
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   70 MET
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain D residue  248 ILE
Chi-restraints excluded: chain D residue  259 VAL
Chi-restraints excluded: chain D residue  272 PRO
Chi-restraints excluded: chain D residue  306 THR
Chi-restraints excluded: chain D residue  340 LEU
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue  111 LEU
Chi-restraints excluded: chain F residue  169 GLU
Chi-restraints excluded: chain F residue  182 VAL
Chi-restraints excluded: chain F residue  202 THR
Chi-restraints excluded: chain F residue  217 TYR
Chi-restraints excluded: chain F residue  271 VAL
Chi-restraints excluded: chain F residue  297 THR
Chi-restraints excluded: chain F residue  377 ASN
Chi-restraints excluded: chain F residue  394 THR
Chi-restraints excluded: chain F residue  423 ILE
Chi-restraints excluded: chain F residue  446 ARG
Chi-restraints excluded: chain F residue  450 THR
Chi-restraints excluded: chain G residue  583 VAL
Chi-restraints excluded: chain G residue  595 ILE
Chi-restraints excluded: chain G residue  615 SER
Chi-restraints excluded: chain G residue  624 ASP
Chi-restraints excluded: chain G residue  647 GLU
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   76 ILE
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain I residue  253 THR
Chi-restraints excluded: chain I residue  259 VAL
Chi-restraints excluded: chain I residue  295 SER
Chi-restraints excluded: chain I residue  340 LEU
Chi-restraints excluded: chain K residue   46 LYS
Chi-restraints excluded: chain K residue   68 VAL
Chi-restraints excluded: chain K residue   85 VAL
Chi-restraints excluded: chain K residue  128 THR
Chi-restraints excluded: chain K residue  182 VAL
Chi-restraints excluded: chain K residue  188 THR
Chi-restraints excluded: chain K residue  215 ILE
Chi-restraints excluded: chain K residue  218 CYS
Chi-restraints excluded: chain K residue  249 HIS
Chi-restraints excluded: chain K residue  288 LEU
Chi-restraints excluded: chain K residue  289 HIS
Chi-restraints excluded: chain K residue  292 VAL
Chi-restraints excluded: chain K residue  445 CYS
Chi-restraints excluded: chain K residue  450 THR
Chi-restraints excluded: chain K residue  501 CYS
Chi-restraints excluded: chain L residue  529 THR
Chi-restraints excluded: chain L residue  580 VAL
Chi-restraints excluded: chain L residue  581 LEU
Chi-restraints excluded: chain L residue  587 LEU
Chi-restraints excluded: chain L residue  592 LEU
Chi-restraints excluded: chain L residue  608 VAL
Chi-restraints excluded: chain L residue  623 TRP
Chi-restraints excluded: chain L residue  630 GLN
Chi-restraints excluded: chain M residue   39 LEU
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain N residue  240 VAL
Chi-restraints excluded: chain N residue  265 VAL
Chi-restraints excluded: chain N residue  339 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 243
   random chunks:
   chunk 226 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 133 optimal weight:    0.8980
   chunk 171 optimal weight:    2.9990
   chunk 197 optimal weight:    7.9990
   chunk 131 optimal weight:    0.4980
   chunk 234 optimal weight:    6.9990
   chunk 146 optimal weight:   10.0000
   chunk 142 optimal weight:    0.7980
   chunk 108 optimal weight:    2.9990
   chunk 144 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C   3 GLN
** F  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 362 ASN
H   6 GLN
** H  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN
** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M   6 GLN
** M  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 269 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.6124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  20463  Z= 0.213
  Angle     :  0.708  12.800  27849  Z= 0.355
  Chirality :  0.046   0.232   3327
  Planarity :  0.004   0.070   3456
  Dihedral  :  7.371  59.327   3954
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.58 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 21.48 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

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: -2.13 (0.16), residues: 2448
  helix: -0.20 (0.30), residues: 330
  sheet: -0.60 (0.19), residues: 660
  loop : -2.20 (0.14), residues: 1458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP M  47 
 HIS   0.004   0.001   HIS A 330 
 PHE   0.019   0.001   PHE M  64 
 TYR   0.021   0.001   TYR L 643 
 ARG   0.004   0.000   ARG M  38 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  418 residues out of total 2142 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 92
    poor density    : 326
  time to evaluate  : 2.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  280 ASN cc_start: 0.8618 (m-40) cc_final: 0.8353 (m-40)
REVERT: A  439 ILE cc_start: 0.9667 (tp) cc_final: 0.9390 (mm)
REVERT: A  490 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8112 (ttmm)
REVERT: B  529 THR cc_start: 0.8972 (p) cc_final: 0.8721 (t)
REVERT: B  530 MET cc_start: 0.9091 (mmm) cc_final: 0.8344 (mpp)
REVERT: B  542 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7654 (ttt-90)
REVERT: B  654 GLU cc_start: 0.7712 (pm20) cc_final: 0.7468 (pm20)
REVERT: B  656 ASN cc_start: 0.8304 (t0) cc_final: 0.8030 (t0)
REVERT: C   10 GLU cc_start: 0.8364 (tp30) cc_final: 0.7756 (tm-30)
REVERT: D  272 PRO cc_start: 0.7681 (OUTLIER) cc_final: 0.7243 (Cg_endo)
REVERT: D  282 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7527 (mt-10)
REVERT: D  301 ASN cc_start: 0.8817 (m-40) cc_final: 0.8592 (t0)
REVERT: D  311 GLN cc_start: 0.8825 (pm20) cc_final: 0.8509 (pm20)
REVERT: D  314 ASP cc_start: 0.7696 (m-30) cc_final: 0.7347 (m-30)
REVERT: D  336 LYS cc_start: 0.8623 (tttp) cc_final: 0.8287 (tptt)
REVERT: F  104 MET cc_start: 0.8987 (ttt) cc_final: 0.8538 (ttt)
REVERT: F  268 LYS cc_start: 0.8627 (ptmt) cc_final: 0.8181 (mttm)
REVERT: F  446 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7781 (ttm110)
REVERT: H   39 LEU cc_start: 0.8340 (mt) cc_final: 0.8089 (mt)
REVERT: I  234 LEU cc_start: 0.7500 (mt) cc_final: 0.7085 (mp)
REVERT: I  268 TYR cc_start: 0.8762 (m-80) cc_final: 0.8454 (m-80)
REVERT: K  104 MET cc_start: 0.8541 (ttt) cc_final: 0.8179 (ttt)
REVERT: K  268 LYS cc_start: 0.8619 (pttt) cc_final: 0.8291 (mmtt)
REVERT: K  280 ASN cc_start: 0.7882 (m-40) cc_final: 0.7619 (t0)
REVERT: K  479 TRP cc_start: 0.8436 (m-10) cc_final: 0.8184 (m-90)
REVERT: L  529 THR cc_start: 0.8806 (OUTLIER) cc_final: 0.8446 (t)
REVERT: L  616 ASN cc_start: 0.7269 (t0) cc_final: 0.7039 (t0)
REVERT: L  623 TRP cc_start: 0.8201 (OUTLIER) cc_final: 0.7806 (t-100)
REVERT: L  633 LYS cc_start: 0.9308 (pptt) cc_final: 0.9044 (pptt)
REVERT: M    6 GLN cc_start: 0.7633 (pt0) cc_final: 0.7040 (pt0)
REVERT: M   10 GLU cc_start: 0.7002 (pm20) cc_final: 0.6710 (pp20)
REVERT: M   59 ASN cc_start: 0.8560 (t0) cc_final: 0.8025 (t0)
REVERT: M  102 ILE cc_start: 0.8251 (mt) cc_final: 0.7805 (pt)
REVERT: N  301 ASN cc_start: 0.8227 (m-40) cc_final: 0.7696 (t0)
  outliers start: 92
  outliers final: 72
  residues processed: 394
  average time/residue: 0.2732
  time to fit residues: 171.9160
Evaluate side-chains
  387 residues out of total 2142 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 77
    poor density    : 310
  time to evaluate  : 2.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  203 GLN
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  446 ARG
Chi-restraints excluded: chain A residue  490 LYS
Chi-restraints excluded: chain B residue  641 ILE
Chi-restraints excluded: chain C residue   28 THR
Chi-restraints excluded: chain C residue   70 MET
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain D residue  248 ILE
Chi-restraints excluded: chain D residue  259 VAL
Chi-restraints excluded: chain D residue  272 PRO
Chi-restraints excluded: chain D residue  306 THR
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue  182 VAL
Chi-restraints excluded: chain F residue  202 THR
Chi-restraints excluded: chain F residue  217 TYR
Chi-restraints excluded: chain F residue  271 VAL
Chi-restraints excluded: chain F residue  345 VAL
Chi-restraints excluded: chain F residue  362 ASN
Chi-restraints excluded: chain F residue  377 ASN
Chi-restraints excluded: chain F residue  446 ARG
Chi-restraints excluded: chain F residue  450 THR
Chi-restraints excluded: chain G residue  583 VAL
Chi-restraints excluded: chain G residue  595 ILE
Chi-restraints excluded: chain G residue  615 SER
Chi-restraints excluded: chain G residue  624 ASP
Chi-restraints excluded: chain G residue  647 GLU
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   76 ILE
Chi-restraints excluded: chain H residue   89 ASP
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue   98 THR
Chi-restraints excluded: chain I residue  259 VAL
Chi-restraints excluded: chain I residue  295 SER
Chi-restraints excluded: chain I residue  340 LEU
Chi-restraints excluded: chain K residue   68 VAL
Chi-restraints excluded: chain K residue   85 VAL
Chi-restraints excluded: chain K residue  170 LYS
Chi-restraints excluded: chain K residue  182 VAL
Chi-restraints excluded: chain K residue  188 THR
Chi-restraints excluded: chain K residue  202 THR
Chi-restraints excluded: chain K residue  215 ILE
Chi-restraints excluded: chain K residue  218 CYS
Chi-restraints excluded: chain K residue  249 HIS
Chi-restraints excluded: chain K residue  288 LEU
Chi-restraints excluded: chain K residue  289 HIS
Chi-restraints excluded: chain K residue  292 VAL
Chi-restraints excluded: chain K residue  293 GLU
Chi-restraints excluded: chain K residue  445 CYS
Chi-restraints excluded: chain K residue  450 THR
Chi-restraints excluded: chain K residue  501 CYS
Chi-restraints excluded: chain L residue  529 THR
Chi-restraints excluded: chain L residue  580 VAL
Chi-restraints excluded: chain L residue  581 LEU
Chi-restraints excluded: chain L residue  587 LEU
Chi-restraints excluded: chain L residue  592 LEU
Chi-restraints excluded: chain L residue  608 VAL
Chi-restraints excluded: chain L residue  623 TRP
Chi-restraints excluded: chain L residue  630 GLN
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain N residue  240 VAL
Chi-restraints excluded: chain N residue  257 TYR
Chi-restraints excluded: chain N residue  265 VAL
Chi-restraints excluded: chain N residue  339 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 243
   random chunks:
   chunk 93 optimal weight:    0.6980
   chunk 139 optimal weight:    3.9990
   chunk 70 optimal weight:    8.9990
   chunk 46 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 148 optimal weight:    1.9990
   chunk 159 optimal weight:    8.9990
   chunk 115 optimal weight:    0.4980
   chunk 21 optimal weight:    2.9990
   chunk 184 optimal weight:    0.0770
   chunk 213 optimal weight:    0.5980
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN
** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.6297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  20463  Z= 0.192
  Angle     :  0.708  12.850  27849  Z= 0.353
  Chirality :  0.046   0.229   3327
  Planarity :  0.004   0.068   3456
  Dihedral  :  7.204  58.468   3954
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.13 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 22.08 %
    Favored  : 74.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -2.09 (0.16), residues: 2448
  helix: -0.19 (0.30), residues: 329
  sheet: -0.57 (0.19), residues: 675
  loop : -2.19 (0.15), residues: 1444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.002   TRP M  47 
 HIS   0.004   0.001   HIS K  72 
 PHE   0.016   0.001   PHE M  64 
 TYR   0.021   0.001   TYR N 318 
 ARG   0.006   0.000   ARG M  38 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  413 residues out of total 2142 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 82
    poor density    : 331
  time to evaluate  : 2.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 MET cc_start: 0.8577 (ttt) cc_final: 0.8230 (tpp)
REVERT: A  217 TYR cc_start: 0.8346 (m-10) cc_final: 0.7442 (m-10)
REVERT: A  280 ASN cc_start: 0.8600 (m-40) cc_final: 0.8346 (m-40)
REVERT: A  439 ILE cc_start: 0.9650 (tp) cc_final: 0.9400 (mm)
REVERT: B  529 THR cc_start: 0.8968 (p) cc_final: 0.8738 (t)
REVERT: B  530 MET cc_start: 0.9038 (mmm) cc_final: 0.8463 (mmm)
REVERT: B  542 ARG cc_start: 0.7901 (ttp80) cc_final: 0.7621 (ttt-90)
REVERT: B  656 ASN cc_start: 0.8313 (t0) cc_final: 0.8060 (t0)
REVERT: C   10 GLU cc_start: 0.8316 (tp30) cc_final: 0.7682 (tm-30)
REVERT: C   51 MET cc_start: 0.8075 (tpp) cc_final: 0.7805 (ttt)
REVERT: D  272 PRO cc_start: 0.7741 (OUTLIER) cc_final: 0.7309 (Cg_endo)
REVERT: D  282 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7513 (mt-10)
REVERT: D  301 ASN cc_start: 0.8864 (m-40) cc_final: 0.8636 (t0)
REVERT: D  311 GLN cc_start: 0.8835 (pm20) cc_final: 0.8512 (pm20)
REVERT: D  314 ASP cc_start: 0.7769 (m-30) cc_final: 0.7354 (m-30)
REVERT: D  336 LYS cc_start: 0.8645 (tttp) cc_final: 0.8401 (tptt)
REVERT: F  104 MET cc_start: 0.9001 (ttt) cc_final: 0.8408 (ttt)
REVERT: F  268 LYS cc_start: 0.8548 (ptmt) cc_final: 0.8073 (mttm)
REVERT: F  282 LYS cc_start: 0.8343 (mtmt) cc_final: 0.8121 (mppt)
REVERT: F  423 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8733 (mp)
REVERT: F  446 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7764 (ttm110)
REVERT: H    3 GLN cc_start: 0.8352 (pm20) cc_final: 0.8146 (pm20)
REVERT: H   43 GLN cc_start: 0.6831 (OUTLIER) cc_final: 0.5607 (pm20)
REVERT: H   89 ASP cc_start: 0.8211 (t70) cc_final: 0.7964 (p0)
REVERT: H   97 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.8061 (m)
REVERT: I  234 LEU cc_start: 0.7486 (mt) cc_final: 0.7090 (mp)
REVERT: I  268 TYR cc_start: 0.8699 (m-80) cc_final: 0.8436 (m-80)
REVERT: K   49 LYS cc_start: 0.8399 (ttpt) cc_final: 0.7769 (mtpt)
REVERT: K  104 MET cc_start: 0.8549 (ttt) cc_final: 0.8217 (ttt)
REVERT: K  268 LYS cc_start: 0.8634 (pttt) cc_final: 0.8256 (mmtt)
REVERT: K  280 ASN cc_start: 0.7882 (m-40) cc_final: 0.7611 (t0)
REVERT: K  479 TRP cc_start: 0.8341 (m-10) cc_final: 0.8125 (m-90)
REVERT: L  529 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8460 (t)
REVERT: L  616 ASN cc_start: 0.7262 (t0) cc_final: 0.7036 (t0)
REVERT: L  623 TRP cc_start: 0.8195 (OUTLIER) cc_final: 0.7805 (t-100)
REVERT: L  633 LYS cc_start: 0.9299 (pptt) cc_final: 0.9037 (pptt)
REVERT: M    6 GLN cc_start: 0.7632 (pt0) cc_final: 0.7066 (pt0)
REVERT: M   10 GLU cc_start: 0.7032 (pm20) cc_final: 0.6775 (pp20)
REVERT: M   13 ASN cc_start: 0.8088 (p0) cc_final: 0.7225 (m-40)
REVERT: M   59 ASN cc_start: 0.8535 (t0) cc_final: 0.7965 (t0)
REVERT: M  102 ILE cc_start: 0.8267 (mt) cc_final: 0.7869 (pt)
REVERT: N  267 TRP cc_start: 0.8216 (m-90) cc_final: 0.7967 (m100)
REVERT: N  301 ASN cc_start: 0.8232 (m-40) cc_final: 0.7650 (t0)
  outliers start: 82
  outliers final: 64
  residues processed: 391
  average time/residue: 0.2857
  time to fit residues: 178.7823
Evaluate side-chains
  381 residues out of total 2142 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 71
    poor density    : 310
  time to evaluate  : 2.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  446 ARG
Chi-restraints excluded: chain B residue  545 LEU
Chi-restraints excluded: chain B residue  641 ILE
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain D residue  248 ILE
Chi-restraints excluded: chain D residue  259 VAL
Chi-restraints excluded: chain D residue  272 PRO
Chi-restraints excluded: chain D residue  306 THR
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue   84 LEU
Chi-restraints excluded: chain F residue  182 VAL
Chi-restraints excluded: chain F residue  202 THR
Chi-restraints excluded: chain F residue  271 VAL
Chi-restraints excluded: chain F residue  297 THR
Chi-restraints excluded: chain F residue  345 VAL
Chi-restraints excluded: chain F residue  377 ASN
Chi-restraints excluded: chain F residue  394 THR
Chi-restraints excluded: chain F residue  423 ILE
Chi-restraints excluded: chain F residue  446 ARG
Chi-restraints excluded: chain F residue  450 THR
Chi-restraints excluded: chain G residue  583 VAL
Chi-restraints excluded: chain G residue  595 ILE
Chi-restraints excluded: chain G residue  615 SER
Chi-restraints excluded: chain G residue  624 ASP
Chi-restraints excluded: chain G residue  647 GLU
Chi-restraints excluded: chain H residue   43 GLN
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   76 ILE
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain I residue  259 VAL
Chi-restraints excluded: chain I residue  295 SER
Chi-restraints excluded: chain I residue  340 LEU
Chi-restraints excluded: chain K residue   68 VAL
Chi-restraints excluded: chain K residue   85 VAL
Chi-restraints excluded: chain K residue  182 VAL
Chi-restraints excluded: chain K residue  188 THR
Chi-restraints excluded: chain K residue  202 THR
Chi-restraints excluded: chain K residue  215 ILE
Chi-restraints excluded: chain K residue  218 CYS
Chi-restraints excluded: chain K residue  249 HIS
Chi-restraints excluded: chain K residue  289 HIS
Chi-restraints excluded: chain K residue  292 VAL
Chi-restraints excluded: chain K residue  293 GLU
Chi-restraints excluded: chain K residue  445 CYS
Chi-restraints excluded: chain K residue  450 THR
Chi-restraints excluded: chain K residue  501 CYS
Chi-restraints excluded: chain L residue  529 THR
Chi-restraints excluded: chain L residue  580 VAL
Chi-restraints excluded: chain L residue  581 LEU
Chi-restraints excluded: chain L residue  587 LEU
Chi-restraints excluded: chain L residue  592 LEU
Chi-restraints excluded: chain L residue  623 TRP
Chi-restraints excluded: chain L residue  630 GLN
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain N residue  257 TYR
Chi-restraints excluded: chain N residue  265 VAL
Chi-restraints excluded: chain N residue  339 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 243
   random chunks:
   chunk 224 optimal weight:    0.7980
   chunk 204 optimal weight:    4.9990
   chunk 218 optimal weight:    0.9990
   chunk 131 optimal weight:    3.9990
   chunk 95 optimal weight:    0.0060
   chunk 171 optimal weight:    0.0270
   chunk 66 optimal weight:    4.9990
   chunk 197 optimal weight:    0.8980
   chunk 206 optimal weight:    2.9990
   chunk 217 optimal weight:    0.7980
   chunk 143 optimal weight:    4.9990
   overall best weight:    0.5054

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

Flipped N/Q/H residues before XYZ refinement:
** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 362 ASN
** G 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  43 GLN
** H  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN
H 119 GLN
** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 246 GLN
** K  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.6455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  20463  Z= 0.186
  Angle     :  0.706  12.845  27849  Z= 0.351
  Chirality :  0.046   0.231   3327
  Planarity :  0.004   0.064   3456
  Dihedral  :  6.987  59.587   3954
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.25 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 22.41 %
    Favored  : 73.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

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: -2.04 (0.16), residues: 2448
  helix: -0.33 (0.30), residues: 343
  sheet: -0.52 (0.19), residues: 678
  loop : -2.13 (0.15), residues: 1427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP D 267 
 HIS   0.004   0.001   HIS K  72 
 PHE   0.018   0.001   PHE H  64 
 TYR   0.019   0.001   TYR N 278 
 ARG   0.003   0.000   ARG B 588 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  407 residues out of total 2142 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 84
    poor density    : 323
  time to evaluate  : 2.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 MET cc_start: 0.8608 (ttt) cc_final: 0.8325 (tpp)
REVERT: A  280 ASN cc_start: 0.8593 (m-40) cc_final: 0.8344 (m-40)
REVERT: A  439 ILE cc_start: 0.9633 (tp) cc_final: 0.9380 (mm)
REVERT: B  529 THR cc_start: 0.8919 (p) cc_final: 0.8695 (t)
REVERT: B  530 MET cc_start: 0.9003 (mmm) cc_final: 0.8406 (mmm)
REVERT: B  542 ARG cc_start: 0.7859 (ttp80) cc_final: 0.7608 (ttt-90)
REVERT: B  626 MET cc_start: 0.6557 (tpp) cc_final: 0.6175 (tpp)
REVERT: B  656 ASN cc_start: 0.8220 (t0) cc_final: 0.7951 (t0)
REVERT: C   10 GLU cc_start: 0.8281 (tp30) cc_final: 0.7772 (tm-30)
REVERT: D  272 PRO cc_start: 0.7755 (OUTLIER) cc_final: 0.7316 (Cg_endo)
REVERT: D  282 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7505 (mt-10)
REVERT: D  314 ASP cc_start: 0.7742 (m-30) cc_final: 0.7238 (m-30)
REVERT: F   84 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7834 (mt)
REVERT: F  104 MET cc_start: 0.8977 (ttt) cc_final: 0.8701 (ttt)
REVERT: F  268 LYS cc_start: 0.8556 (ptmt) cc_final: 0.8184 (mmtm)
REVERT: F  282 LYS cc_start: 0.8305 (mtmt) cc_final: 0.8085 (mppt)
REVERT: F  423 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8754 (mp)
REVERT: F  446 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7772 (ttm110)
REVERT: H    3 GLN cc_start: 0.8349 (pm20) cc_final: 0.8130 (pm20)
REVERT: H   43 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.5773 (pm20)
REVERT: H   47 TRP cc_start: 0.8279 (t60) cc_final: 0.8039 (t60)
REVERT: H   97 VAL cc_start: 0.8325 (OUTLIER) cc_final: 0.8065 (m)
REVERT: I  234 LEU cc_start: 0.7523 (mt) cc_final: 0.7147 (mp)
REVERT: I  268 TYR cc_start: 0.8713 (m-80) cc_final: 0.8462 (m-80)
REVERT: K   49 LYS cc_start: 0.8331 (ttpt) cc_final: 0.7711 (mtpt)
REVERT: K  104 MET cc_start: 0.8556 (ttt) cc_final: 0.8240 (ttt)
REVERT: K  268 LYS cc_start: 0.8687 (pttt) cc_final: 0.8361 (mmtt)
REVERT: K  280 ASN cc_start: 0.8089 (m-40) cc_final: 0.7830 (t0)
REVERT: K  479 TRP cc_start: 0.8335 (m-10) cc_final: 0.8128 (m-90)
REVERT: L  529 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8474 (t)
REVERT: L  623 TRP cc_start: 0.8190 (OUTLIER) cc_final: 0.7825 (t-100)
REVERT: L  633 LYS cc_start: 0.9310 (pptt) cc_final: 0.9035 (pptt)
REVERT: M   10 GLU cc_start: 0.7087 (pm20) cc_final: 0.6825 (pp20)
REVERT: M   13 ASN cc_start: 0.7978 (p0) cc_final: 0.7322 (m-40)
REVERT: M   59 ASN cc_start: 0.8534 (t0) cc_final: 0.7965 (t0)
REVERT: M  102 ILE cc_start: 0.8276 (mt) cc_final: 0.7884 (pt)
REVERT: N  299 SER cc_start: 0.9111 (OUTLIER) cc_final: 0.8818 (p)
REVERT: N  301 ASN cc_start: 0.8290 (m-40) cc_final: 0.7807 (t0)
  outliers start: 84
  outliers final: 67
  residues processed: 388
  average time/residue: 0.2692
  time to fit residues: 167.8577
Evaluate side-chains
  391 residues out of total 2142 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 76
    poor density    : 315
  time to evaluate  : 2.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  326 ILE
Chi-restraints excluded: chain B residue  545 LEU
Chi-restraints excluded: chain B residue  641 ILE
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain D residue  248 ILE
Chi-restraints excluded: chain D residue  259 VAL
Chi-restraints excluded: chain D residue  272 PRO
Chi-restraints excluded: chain D residue  306 THR
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue   84 LEU
Chi-restraints excluded: chain F residue  120 VAL
Chi-restraints excluded: chain F residue  169 GLU
Chi-restraints excluded: chain F residue  182 VAL
Chi-restraints excluded: chain F residue  202 THR
Chi-restraints excluded: chain F residue  271 VAL
Chi-restraints excluded: chain F residue  297 THR
Chi-restraints excluded: chain F residue  362 ASN
Chi-restraints excluded: chain F residue  377 ASN
Chi-restraints excluded: chain F residue  394 THR
Chi-restraints excluded: chain F residue  423 ILE
Chi-restraints excluded: chain F residue  426 MET
Chi-restraints excluded: chain F residue  446 ARG
Chi-restraints excluded: chain F residue  450 THR
Chi-restraints excluded: chain G residue  583 VAL
Chi-restraints excluded: chain G residue  595 ILE
Chi-restraints excluded: chain G residue  615 SER
Chi-restraints excluded: chain G residue  624 ASP
Chi-restraints excluded: chain H residue   43 GLN
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   76 ILE
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain I residue  259 VAL
Chi-restraints excluded: chain I residue  295 SER
Chi-restraints excluded: chain K residue   68 VAL
Chi-restraints excluded: chain K residue   85 VAL
Chi-restraints excluded: chain K residue  157 CYS
Chi-restraints excluded: chain K residue  170 LYS
Chi-restraints excluded: chain K residue  182 VAL
Chi-restraints excluded: chain K residue  188 THR
Chi-restraints excluded: chain K residue  202 THR
Chi-restraints excluded: chain K residue  215 ILE
Chi-restraints excluded: chain K residue  218 CYS
Chi-restraints excluded: chain K residue  249 HIS
Chi-restraints excluded: chain K residue  289 HIS
Chi-restraints excluded: chain K residue  292 VAL
Chi-restraints excluded: chain K residue  293 GLU
Chi-restraints excluded: chain K residue  445 CYS
Chi-restraints excluded: chain K residue  450 THR
Chi-restraints excluded: chain K residue  501 CYS
Chi-restraints excluded: chain L residue  529 THR
Chi-restraints excluded: chain L residue  580 VAL
Chi-restraints excluded: chain L residue  581 LEU
Chi-restraints excluded: chain L residue  587 LEU
Chi-restraints excluded: chain L residue  623 TRP
Chi-restraints excluded: chain L residue  630 GLN
Chi-restraints excluded: chain M residue   39 LEU
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain N residue  257 TYR
Chi-restraints excluded: chain N residue  265 VAL
Chi-restraints excluded: chain N residue  299 SER
Chi-restraints excluded: chain N residue  315 GLU
Chi-restraints excluded: chain N residue  339 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 243
   random chunks:
   chunk 230 optimal weight:    3.9990
   chunk 140 optimal weight:    5.9990
   chunk 109 optimal weight:    2.9990
   chunk 160 optimal weight:    2.9990
   chunk 242 optimal weight:    4.9990
   chunk 222 optimal weight:    0.9990
   chunk 192 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 148 optimal weight:    4.9990
   chunk 118 optimal weight:    0.8980
   chunk 153 optimal weight:    4.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 114 GLN
** F  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 287 HIS
F 362 ASN
H  63 ASN
** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 287 HIS
** L 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 246 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.6811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.077  20463  Z= 0.418
  Angle     :  0.824  13.011  27849  Z= 0.413
  Chirality :  0.050   0.309   3327
  Planarity :  0.005   0.067   3456
  Dihedral  :  7.432  59.572   3954
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.80 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 22.41 %
    Favored  : 73.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -2.15 (0.16), residues: 2448
  helix: -0.28 (0.30), residues: 336
  sheet: -0.78 (0.18), residues: 696
  loop : -2.13 (0.15), residues: 1416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.066   0.003   TRP D 267 
 HIS   0.008   0.002   HIS A 330 
 PHE   0.026   0.002   PHE H  64 
 TYR   0.028   0.002   TYR B 643 
 ARG   0.005   0.001   ARG F 298 

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

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

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4896 Ramachandran restraints generated.
    2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  397 residues out of total 2142 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 84
    poor density    : 313
  time to evaluate  : 2.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  217 TYR cc_start: 0.8427 (m-10) cc_final: 0.8172 (m-10)
REVERT: A  280 ASN cc_start: 0.8682 (m-40) cc_final: 0.8217 (t0)
REVERT: A  439 ILE cc_start: 0.9642 (tp) cc_final: 0.9406 (mm)
REVERT: B  529 THR cc_start: 0.8869 (p) cc_final: 0.8663 (t)
REVERT: B  530 MET cc_start: 0.9057 (mmm) cc_final: 0.8361 (mmm)
REVERT: B  542 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7705 (ttt-90)
REVERT: B  581 LEU cc_start: 0.8040 (tp) cc_final: 0.7631 (tp)
REVERT: B  626 MET cc_start: 0.6716 (tpp) cc_final: 0.6284 (tpp)
REVERT: B  632 ASP cc_start: 0.8635 (t70) cc_final: 0.8362 (t0)
REVERT: B  656 ASN cc_start: 0.8299 (t0) cc_final: 0.8029 (t0)
REVERT: C   10 GLU cc_start: 0.8281 (tp30) cc_final: 0.7835 (tm-30)
REVERT: D  282 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7478 (mt-10)
REVERT: D  314 ASP cc_start: 0.7711 (m-30) cc_final: 0.7474 (m-30)
REVERT: F   84 LEU cc_start: 0.8219 (tp) cc_final: 0.7852 (mt)
REVERT: F  104 MET cc_start: 0.9027 (ttt) cc_final: 0.8449 (ttt)
REVERT: F  195 ASN cc_start: 0.8173 (t0) cc_final: 0.7946 (t0)
REVERT: F  268 LYS cc_start: 0.8601 (ptmt) cc_final: 0.8215 (mttm)
REVERT: F  282 LYS cc_start: 0.8431 (mtmt) cc_final: 0.8154 (mppt)
REVERT: F  423 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8815 (mp)
REVERT: F  446 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7864 (ttm110)
REVERT: H    3 GLN cc_start: 0.8385 (pm20) cc_final: 0.8147 (pm20)
REVERT: H   43 GLN cc_start: 0.6870 (pp30) cc_final: 0.5833 (pm20)
REVERT: H   47 TRP cc_start: 0.8514 (t60) cc_final: 0.7992 (t60)
REVERT: I  234 LEU cc_start: 0.7730 (mt) cc_final: 0.7351 (mp)
REVERT: K   49 LYS cc_start: 0.8436 (ttpt) cc_final: 0.7857 (mtpt)
REVERT: K  268 LYS cc_start: 0.8687 (pttt) cc_final: 0.8420 (mmtt)
REVERT: K  369 MET cc_start: 0.7433 (tpp) cc_final: 0.6867 (ttt)
REVERT: L  529 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8661 (t)
REVERT: L  623 TRP cc_start: 0.8363 (OUTLIER) cc_final: 0.8010 (t-100)
REVERT: L  624 ASP cc_start: 0.8075 (t0) cc_final: 0.7804 (m-30)
REVERT: L  633 LYS cc_start: 0.9341 (pptt) cc_final: 0.9105 (pptt)
REVERT: M   10 GLU cc_start: 0.7402 (pm20) cc_final: 0.6929 (pp20)
REVERT: M   13 ASN cc_start: 0.8038 (p0) cc_final: 0.7384 (m110)
REVERT: M   59 ASN cc_start: 0.8742 (t0) cc_final: 0.8014 (t0)
REVERT: M  102 ILE cc_start: 0.8468 (mt) cc_final: 0.8023 (pt)
REVERT: N  299 SER cc_start: 0.9187 (OUTLIER) cc_final: 0.8900 (p)
REVERT: N  301 ASN cc_start: 0.8537 (m-40) cc_final: 0.7972 (t0)
  outliers start: 84
  outliers final: 71
  residues processed: 375
  average time/residue: 0.2710
  time to fit residues: 163.3773
Evaluate side-chains
  374 residues out of total 2142 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 76
    poor density    : 298
  time to evaluate  : 2.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  102 ASP
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  446 ARG
Chi-restraints excluded: chain B residue  545 LEU
Chi-restraints excluded: chain B residue  641 ILE
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   97 VAL
Chi-restraints excluded: chain D residue  248 ILE
Chi-restraints excluded: chain D residue  259 VAL
Chi-restraints excluded: chain D residue  306 THR
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue  120 VAL
Chi-restraints excluded: chain F residue  182 VAL
Chi-restraints excluded: chain F residue  202 THR
Chi-restraints excluded: chain F residue  215 ILE
Chi-restraints excluded: chain F residue  271 VAL
Chi-restraints excluded: chain F residue  297 THR
Chi-restraints excluded: chain F residue  345 VAL
Chi-restraints excluded: chain F residue  362 ASN
Chi-restraints excluded: chain F residue  377 ASN
Chi-restraints excluded: chain F residue  423 ILE
Chi-restraints excluded: chain F residue  426 MET
Chi-restraints excluded: chain F residue  446 ARG
Chi-restraints excluded: chain F residue  450 THR
Chi-restraints excluded: chain G residue  583 VAL
Chi-restraints excluded: chain G residue  595 ILE
Chi-restraints excluded: chain G residue  615 SER
Chi-restraints excluded: chain G residue  624 ASP
Chi-restraints excluded: chain G residue  647 GLU
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain H residue   74 THR
Chi-restraints excluded: chain H residue   76 ILE
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain I residue  259 VAL
Chi-restraints excluded: chain I residue  295 SER
Chi-restraints excluded: chain K residue   68 VAL
Chi-restraints excluded: chain K residue   85 VAL
Chi-restraints excluded: chain K residue  157 CYS
Chi-restraints excluded: chain K residue  170 LYS
Chi-restraints excluded: chain K residue  182 VAL
Chi-restraints excluded: chain K residue  188 THR
Chi-restraints excluded: chain K residue  202 THR
Chi-restraints excluded: chain K residue  215 ILE
Chi-restraints excluded: chain K residue  218 CYS
Chi-restraints excluded: chain K residue  292 VAL
Chi-restraints excluded: chain K residue  293 GLU
Chi-restraints excluded: chain K residue  445 CYS
Chi-restraints excluded: chain K residue  450 THR
Chi-restraints excluded: chain K residue  501 CYS
Chi-restraints excluded: chain L residue  529 THR
Chi-restraints excluded: chain L residue  580 VAL
Chi-restraints excluded: chain L residue  581 LEU
Chi-restraints excluded: chain L residue  587 LEU
Chi-restraints excluded: chain L residue  592 LEU
Chi-restraints excluded: chain L residue  595 ILE
Chi-restraints excluded: chain L residue  623 TRP
Chi-restraints excluded: chain L residue  630 GLN
Chi-restraints excluded: chain M residue   39 LEU
Chi-restraints excluded: chain M residue   97 VAL
Chi-restraints excluded: chain M residue  115 ASP
Chi-restraints excluded: chain N residue  240 VAL
Chi-restraints excluded: chain N residue  265 VAL
Chi-restraints excluded: chain N residue  299 SER
Chi-restraints excluded: chain N residue  315 GLU
Chi-restraints excluded: chain N residue  339 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 243
   random chunks:
   chunk 205 optimal weight:    1.9990
   chunk 59 optimal weight:    8.9990
   chunk 177 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 193 optimal weight:    0.5980
   chunk 80 optimal weight:    6.9990
   chunk 198 optimal weight:    9.9990
   chunk 24 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 169 optimal weight:    2.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 362 ASN
H  43 GLN
H  63 ASN
** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 287 HIS
L 575 GLN
L 616 ASN
M   6 GLN
** M  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.140049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.110529 restraints weight = 43483.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.111026 restraints weight = 35104.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.112315 restraints weight = 29091.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.6911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  20463  Z= 0.249
  Angle     :  0.749  12.681  27849  Z= 0.375
  Chirality :  0.047   0.290   3327
  Planarity :  0.005   0.050   3456
  Dihedral  :  7.249  58.995   3954
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.78 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 23.44 %
    Favored  : 73.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.38 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

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: -2.14 (0.16), residues: 2448
  helix: -0.39 (0.29), residues: 357
  sheet: -0.67 (0.18), residues: 705
  loop : -2.19 (0.15), residues: 1386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.079   0.002   TRP M  47 
 HIS   0.004   0.001   HIS F 249 
 PHE   0.016   0.002   PHE M  64 
 TYR   0.027   0.002   TYR B 643 
 ARG   0.004   0.000   ARG M  72 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4461.40 seconds
wall clock time: 80 minutes 46.97 seconds (4846.97 seconds total)