Starting phenix.real_space_refine
on Mon Jan 20 19:01:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xnh_38504/01_2025/8xnh_38504.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xnh_38504/01_2025/8xnh_38504.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xnh_38504/01_2025/8xnh_38504.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xnh_38504/01_2025/8xnh_38504.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xnh_38504/01_2025/8xnh_38504.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xnh_38504/01_2025/8xnh_38504.cif"
  }
  resolution = 2.3
  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=   0.026
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      72      5.16       5
     C    9962      2.51       5
     N    2568      2.21       5
     O    3104      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 15706
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 3367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 438, 3367
          Classifications: {'peptide': 438}
          Link IDs: {'PTRANS': 15, 'TRANS': 422}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 815
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99}
    Chain: "E"
      Number of atoms: 822
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 822
          Classifications: {'peptide': 108}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100}
    Chain: "F"
      Number of atoms: 859
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 859
          Classifications: {'peptide': 114}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 6, 'TRANS': 104}
    Chain: "G"
      Number of atoms: 1012
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1012
          Classifications: {'peptide': 130}
          Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 122}
    Chain: "H"
      Number of atoms: 1001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 1001
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 6, 'TRANS': 121}
    Chain: "I"
      Number of atoms: 1012
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1012
          Classifications: {'peptide': 130}
          Link IDs: {'PTRANS': 6, 'TRANS': 123}
    Chain: "B"
      Number of atoms: 3367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 438, 3367
          Classifications: {'peptide': 438}
          Link IDs: {'PTRANS': 15, 'TRANS': 422}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 3367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 438, 3367
          Classifications: {'peptide': 438}
          Link IDs: {'PTRANS': 15, 'TRANS': 422}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Residues with excluded nonbonded symmetry interactions: 343
    residue:
      pdb=" N   ASP D   1 " occ=0.71
      ... (6 atoms not shown)
      pdb=" OD2 ASP D   1 " occ=0.02
    residue:
      pdb=" N   GLN D   3 " occ=0.88
      ... (7 atoms not shown)
      pdb=" NE2 GLN D   3 " occ=0.63
    residue:
      pdb=" N   THR D   5 " occ=0.40
      ... (5 atoms not shown)
      pdb=" CG2 THR D   5 " occ=0.82
    residue:
      pdb=" N   GLN D   6 " occ=0.44
      ... (7 atoms not shown)
      pdb=" NE2 GLN D   6 " occ=0.21
    residue:
      pdb=" N   SER D   7 " occ=0.00
      ... (4 atoms not shown)
      pdb=" OG  SER D   7 " occ=0.42
    residue:
      pdb=" N   PRO D   8 " occ=0.00
      ... (5 atoms not shown)
      pdb=" CD  PRO D   8 " occ=0.58
    residue:
      pdb=" N   SER D   9 " occ=0.24
      ... (4 atoms not shown)
      pdb=" OG  SER D   9 " occ=0.00
    residue:
      pdb=" N   SER D  10 " occ=0.10
      ... (4 atoms not shown)
      pdb=" OG  SER D  10 " occ=0.32
    residue:
      pdb=" N   LEU D  11 " occ=0.24
      ... (6 atoms not shown)
      pdb=" CD2 LEU D  11 " occ=0.54
    residue:
      pdb=" N   SER D  12 " occ=0.11
      ... (4 atoms not shown)
      pdb=" OG  SER D  12 " occ=0.28
    residue:
      pdb=" N   ALA D  13 " occ=0.26
      ... (3 atoms not shown)
      pdb=" CB  ALA D  13 " occ=0.68
    residue:
      pdb=" N   SER D  14 " occ=0.19
      ... (4 atoms not shown)
      pdb=" OG  SER D  14 " occ=0.50
    ... (remaining 331 not shown)
  Time building chain proxies: 11.64, per 1000 atoms: 0.74
  Number of scatterers: 15706
  At special positions: 0
  Unit cell: (107.07, 142.76, 155.21, 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      72     16.00
     O    3104      8.00
     N    2568      7.00
     C    9962      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=21, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  71 " - pdb=" SG  CYS A 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 331 " - pdb=" SG  CYS A 340 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 355 " - pdb=" SG  CYS A 363 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 387 " - pdb=" SG  CYS A 392 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 394 " - pdb=" SG  CYS A 417 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  87 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  23 " - pdb=" SG  CYS E  87 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  23 " - pdb=" SG  CYS F  87 " distance=2.05
    Simple disulfide: pdb=" SG  CYS G  22 " - pdb=" SG  CYS G  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  22 " - pdb=" SG  CYS I  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  71 " - pdb=" SG  CYS B 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 331 " - pdb=" SG  CYS B 340 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 355 " - pdb=" SG  CYS B 363 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 387 " - pdb=" SG  CYS B 392 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 394 " - pdb=" SG  CYS B 417 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  71 " - pdb=" SG  CYS C 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 331 " - pdb=" SG  CYS C 340 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 355 " - pdb=" SG  CYS C 363 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 387 " - pdb=" SG  CYS C 392 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 394 " - pdb=" SG  CYS C 417 " distance=2.04

  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
    NAG-ASN
      " NAG A 601 " - " ASN A  99 "
      " NAG A 602 " - " ASN A 414 "
      " NAG B 601 " - " ASN B  99 "
      " NAG B 602 " - " ASN B 414 "
      " NAG C 601 " - " ASN C  99 "
      " NAG C 602 " - " ASN C 414 "
  Time building additional restraints: 3.89
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  4014 Ramachandran restraints generated.
    2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3792

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 32 sheets defined
      28.0% alpha, 33.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 36
      removed outlier: 3.572A  pdb=" N   ILE A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 72
      removed outlier: 3.791A  pdb=" N   SER A  69 " --> pdb=" O   SER A  66 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   GLN A  70 " --> pdb=" O   ASN A  67 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   THR A  72 " --> pdb=" O   SER A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 99
      removed outlier: 3.745A  pdb=" N   ASN A  78 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
      Proline residue:  A  89  - end of helix
      removed outlier: 3.740A  pdb=" N   ILE A  96 " --> pdb=" O   GLY A  92 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   TYR A  97 " --> pdb=" O   ALA A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 121
    Processing helix  chain 'A' and resid 125 through 145
      removed outlier: 4.544A  pdb=" N   LYS A 139 " --> pdb=" O   TYR A 135 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   ASN A 140 " --> pdb=" O   GLU A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 154
    Processing helix  chain 'A' and resid 175 through 182
    Processing helix  chain 'A' and resid 183 through 187
      removed outlier: 3.661A  pdb=" N   ILE A 187 " --> pdb=" O   VAL A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 215
      removed outlier: 4.754A  pdb=" N   PHE A 212 " --> pdb=" O   SER A 208 " (cutoff:3.500A)
      removed outlier: 5.128A  pdb=" N   VAL A 213 " --> pdb=" O   ASP A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 232
    Processing helix  chain 'A' and resid 233 through 236
    Processing helix  chain 'A' and resid 238 through 246
      removed outlier: 3.717A  pdb=" N   LEU A 242 " --> pdb=" O   ASN A 238 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU A 246 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 259
    Processing helix  chain 'A' and resid 328 through 331
    Processing helix  chain 'A' and resid 349 through 356
    Processing helix  chain 'A' and resid 357 through 358
      No H-bonds generated for 'chain 'A' and resid 357 through 358'
    Processing helix  chain 'A' and resid 359 through 363
    Processing helix  chain 'A' and resid 437 through 441
      removed outlier: 3.500A  pdb=" N   GLU A 441 " --> pdb=" O   TYR A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 471
      removed outlier: 3.820A  pdb=" N   SER A 457 " --> pdb=" O   LYS A 453 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLN A 469 " --> pdb=" O   GLN A 465 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   SER A 470 " --> pdb=" O   SER A 466 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 63 through 66
    Processing helix  chain 'G' and resid 88 through 92
      removed outlier: 3.735A  pdb=" N   THR G  92 " --> pdb=" O   ALA G  89 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 88 through 92
    Processing helix  chain 'I' and resid 65 through 69
      removed outlier: 3.520A  pdb=" N   VAL I  69 " --> pdb=" O   LYS I  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 36
      removed outlier: 3.561A  pdb=" N   ILE B  36 " --> pdb=" O   LYS B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 72
      removed outlier: 3.882A  pdb=" N   SER B  69 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   GLN B  70 " --> pdb=" O   ASN B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 99
      removed outlier: 3.889A  pdb=" N   ASN B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      Proline residue:  B  89  - end of helix
      removed outlier: 3.648A  pdb=" N   ILE B  96 " --> pdb=" O   GLY B  92 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   TYR B  97 " --> pdb=" O   ALA B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 121
    Processing helix  chain 'B' and resid 125 through 145
      removed outlier: 4.489A  pdb=" N   LYS B 139 " --> pdb=" O   TYR B 135 " (cutoff:3.500A)
      removed outlier: 5.034A  pdb=" N   ASN B 140 " --> pdb=" O   GLU B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 154
      removed outlier: 3.514A  pdb=" N   THR B 154 " --> pdb=" O   SER B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 182
    Processing helix  chain 'B' and resid 183 through 187
      removed outlier: 3.543A  pdb=" N   THR B 186 " --> pdb=" O   LEU B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 215
      removed outlier: 4.809A  pdb=" N   PHE B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
      removed outlier: 5.149A  pdb=" N   VAL B 213 " --> pdb=" O   ASP B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 232
    Processing helix  chain 'B' and resid 233 through 236
    Processing helix  chain 'B' and resid 238 through 246
      removed outlier: 3.903A  pdb=" N   LEU B 242 " --> pdb=" O   ASN B 238 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU B 246 " --> pdb=" O   LEU B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 259
    Processing helix  chain 'B' and resid 328 through 331
    Processing helix  chain 'B' and resid 349 through 357
    Processing helix  chain 'B' and resid 359 through 363
    Processing helix  chain 'B' and resid 437 through 441
      removed outlier: 3.511A  pdb=" N   SER B 440 " --> pdb=" O   ASN B 437 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLU B 441 " --> pdb=" O   TYR B 438 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 437 through 441'
    Processing helix  chain 'B' and resid 452 through 471
      removed outlier: 3.766A  pdb=" N   SER B 457 " --> pdb=" O   LYS B 453 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 35
    Processing helix  chain 'C' and resid 65 through 72
      removed outlier: 3.526A  pdb=" N   SER C  69 " --> pdb=" O   SER C  66 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   GLN C  70 " --> pdb=" O   ASN C  67 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   THR C  72 " --> pdb=" O   SER C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 100
      removed outlier: 3.582A  pdb=" N   ASN C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      Proline residue:  C  89  - end of helix
      removed outlier: 3.816A  pdb=" N   ILE C  96 " --> pdb=" O   GLY C  92 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   TYR C  97 " --> pdb=" O   ALA C  93 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ASN C 100 " --> pdb=" O   ILE C  96 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 121
    Processing helix  chain 'C' and resid 125 through 145
      removed outlier: 4.206A  pdb=" N   LYS C 139 " --> pdb=" O   TYR C 135 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   ASN C 140 " --> pdb=" O   GLU C 136 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ASP C 142 " --> pdb=" O   MET C 138 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ASN C 143 " --> pdb=" O   LYS C 139 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 147 through 153
    Processing helix  chain 'C' and resid 175 through 182
    Processing helix  chain 'C' and resid 183 through 187
      removed outlier: 3.637A  pdb=" N   THR C 186 " --> pdb=" O   LEU C 183 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ILE C 187 " --> pdb=" O   VAL C 184 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 183 through 187'
    Processing helix  chain 'C' and resid 191 through 215
      removed outlier: 4.762A  pdb=" N   PHE C 212 " --> pdb=" O   SER C 208 " (cutoff:3.500A)
      removed outlier: 5.137A  pdb=" N   VAL C 213 " --> pdb=" O   ASP C 209 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 228 through 232
    Processing helix  chain 'C' and resid 233 through 236
    Processing helix  chain 'C' and resid 238 through 246
      removed outlier: 3.853A  pdb=" N   LEU C 242 " --> pdb=" O   ASN C 238 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU C 246 " --> pdb=" O   LEU C 242 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 252 through 259
    Processing helix  chain 'C' and resid 328 through 331
    Processing helix  chain 'C' and resid 349 through 357
      removed outlier: 3.557A  pdb=" N   THR C 357 " --> pdb=" O   ARG C 353 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 359 through 363
      removed outlier: 3.519A  pdb=" N   LYS C 362 " --> pdb=" O   SER C 359 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 437 through 441
    Processing helix  chain 'C' and resid 452 through 471
      removed outlier: 3.912A  pdb=" N   SER C 457 " --> pdb=" O   LYS C 453 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 162
      removed outlier: 17.835A  pdb=" N   THR A 168 " --> pdb=" O   PRO A  52 " (cutoff:3.500A)
      removed outlier: 12.290A  pdb=" N   THR A  54 " --> pdb=" O   THR A 168 " (cutoff:3.500A)
      removed outlier: 11.931A  pdb=" N   TYR A 170 " --> pdb=" O   THR A  54 " (cutoff:3.500A)
      removed outlier: 8.121A  pdb=" N   ASP A  56 " --> pdb=" O   TYR A 170 " (cutoff:3.500A)
      removed outlier: 9.143A  pdb=" N   LEU A 172 " --> pdb=" O   ASP A  56 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   VAL A  58 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   VAL A 338 " --> pdb=" O   THR A  43 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   LYS A  45 " --> pdb=" O   VAL A 338 " (cutoff:3.500A)
      removed outlier: 7.813A  pdb=" N   CYS A 340 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   LYS A  47 " --> pdb=" O   CYS A 340 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227
      removed outlier: 4.280A  pdb=" N   MET A 226 " --> pdb=" O   GLY A 264 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   THR A 263 " --> pdb=" O   TYR A 281 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   ILE A 277 " --> pdb=" O   ILE A 267 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   VAL A 269 " --> pdb=" O   TYR A 275 " (cutoff:3.500A)
      removed outlier: 7.171A  pdb=" N   TYR A 275 " --> pdb=" O   VAL A 269 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   ILE A 284 " --> pdb=" O   ASN A  51 " (cutoff:3.500A)
      removed outlier: 5.384A  pdb=" N   ASN A  51 " --> pdb=" O   ILE A 284 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   THR A 286 " --> pdb=" O   LYS A  49 " (cutoff:3.500A)
      removed outlier: 5.653A  pdb=" N   LYS A  49 " --> pdb=" O   THR A 286 " (cutoff:3.500A)
      removed outlier: 5.613A  pdb=" N   GLU A 295 " --> pdb=" O   GLY A  41 " (cutoff:3.500A)
      removed outlier: 4.821A  pdb=" N   THR A  43 " --> pdb=" O   ILE A 293 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   ILE A 293 " --> pdb=" O   THR A  43 " (cutoff:3.500A)
      removed outlier: 5.534A  pdb=" N   LYS A  45 " --> pdb=" O   ALA A 291 " (cutoff:3.500A)
      removed outlier: 8.340A  pdb=" N   ALA A 291 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   PHE A 315 " --> pdb=" O   ILE A 326 " (cutoff:3.500A)
      removed outlier: 4.830A  pdb=" N   ILE A 326 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102
    Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124
    Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 302
    Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412
    Processing sheet with id=AA7, first strand: chain 'A' and resid 399 through 400
      removed outlier: 6.796A  pdb=" N   ILE A 426 " --> pdb=" O   MET C 115 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 20 through 24
    Processing sheet with id=AA9, first strand: chain 'D' and resid 53 through 54
      removed outlier: 5.698A  pdb=" N   LEU D  46 " --> pdb=" O   GLN D  37 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   GLN D  37 " --> pdb=" O   LEU D  46 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 4 through 7
      removed outlier: 3.652A  pdb=" N   THR E  22 " --> pdb=" O   SER E   7 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   VAL E  19 " --> pdb=" O   ILE E  75 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   ASP E  70 " --> pdb=" O   SER E  67 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 45 through 46
      removed outlier: 3.530A  pdb=" N   TYR E  86 " --> pdb=" O   TYR E  36 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ALA E  84 " --> pdb=" O   GLN E  38 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   THR E  96 " --> pdb=" O   GLN E  89 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 48 through 49
    Processing sheet with id=AB4, first strand: chain 'F' and resid 4 through 7
      removed outlier: 3.580A  pdb=" N   ILE F  75 " --> pdb=" O   VAL F  19 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 12 through 13
      removed outlier: 3.544A  pdb=" N   ALA F  13 " --> pdb=" O   ASP F 104 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'F' and resid 45 through 48
      removed outlier: 6.921A  pdb=" N   TRP F  35 " --> pdb=" O   LEU F  47 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   THR F  96 " --> pdb=" O   GLN F  89 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'G' and resid 3 through 7
      removed outlier: 3.561A  pdb=" N   LEU G  20 " --> pdb=" O   LEU G  82 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   PHE G  80 " --> pdb=" O   CYS G  22 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'G' and resid 11 through 12
      removed outlier: 3.546A  pdb=" N   VAL G  12 " --> pdb=" O   THR G 126 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ARG G  34 " --> pdb=" O   VAL G 100 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   GLY G  50 " --> pdb=" O   TRP G  37 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   ARG G  39 " --> pdb=" O   TRP G  48 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   TRP G  48 " --> pdb=" O   ARG G  39 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'G' and resid 11 through 12
      removed outlier: 3.546A  pdb=" N   VAL G  12 " --> pdb=" O   THR G 126 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   CYS G  97 " --> pdb=" O   TRP G 119 " (cutoff:3.500A)
      removed outlier: 4.928A  pdb=" N   TRP G 119 " --> pdb=" O   CYS G  97 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   ARG G  99 " --> pdb=" O   ASP G 117 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.625A  pdb=" N   SER H  72 " --> pdb=" O   SER H  81 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.664A  pdb=" N   ALA H  93 " --> pdb=" O   VAL H 125 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ILE H  38 " --> pdb=" O   TYR H  96 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ARG H  34 " --> pdb=" O   VAL H 100 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   GLY H  50 " --> pdb=" O   TRP H  37 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ARG H  39 " --> pdb=" O   TRP H  48 " (cutoff:3.500A)
      removed outlier: 5.435A  pdb=" N   TRP H  48 " --> pdb=" O   ARG H  39 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ASN H  60 " --> pdb=" O   TYR H  51 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.664A  pdb=" N   ALA H  93 " --> pdb=" O   VAL H 125 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ARG H  99 " --> pdb=" O   ASP H 117 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'I' and resid 3 through 5
      removed outlier: 3.589A  pdb=" N   GLN I   5 " --> pdb=" O   ALA I  23 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   SER I  72 " --> pdb=" O   SER I  81 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'I' and resid 11 through 12
      removed outlier: 3.689A  pdb=" N   VAL I 123 " --> pdb=" O   TYR I  95 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   VAL I 125 " --> pdb=" O   ALA I  93 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   ALA I  93 " --> pdb=" O   VAL I 125 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ARG I  34 " --> pdb=" O   VAL I 100 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   GLY I  50 " --> pdb=" O   TRP I  37 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   ARG I  39 " --> pdb=" O   TRP I  48 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   TRP I  48 " --> pdb=" O   ARG I  39 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'I' and resid 11 through 12
      removed outlier: 3.689A  pdb=" N   VAL I 123 " --> pdb=" O   TYR I  95 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   VAL I 125 " --> pdb=" O   ALA I  93 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   ALA I  93 " --> pdb=" O   VAL I 125 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   ARG I  99 " --> pdb=" O   ASP I 117 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASP I 117 " --> pdb=" O   ARG I  99 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 158 through 160
      removed outlier: 11.950A  pdb=" N   TYR B 170 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
      removed outlier: 8.114A  pdb=" N   ASP B  56 " --> pdb=" O   TYR B 170 " (cutoff:3.500A)
      removed outlier: 9.119A  pdb=" N   LEU B 172 " --> pdb=" O   ASP B  56 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   VAL B  58 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 7.910A  pdb=" N   VAL B 338 " --> pdb=" O   THR B  43 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   LYS B  45 " --> pdb=" O   VAL B 338 " (cutoff:3.500A)
      removed outlier: 7.803A  pdb=" N   CYS B 340 " --> pdb=" O   LYS B  45 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   LYS B  47 " --> pdb=" O   CYS B 340 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 263 through 270
      removed outlier: 6.676A  pdb=" N   ILE B 277 " --> pdb=" O   ILE B 267 " (cutoff:3.500A)
      removed outlier: 4.973A  pdb=" N   VAL B 269 " --> pdb=" O   TYR B 275 " (cutoff:3.500A)
      removed outlier: 7.165A  pdb=" N   TYR B 275 " --> pdb=" O   VAL B 269 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   ILE B 276 " --> pdb=" O   VAL B  58 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   VAL B  58 " --> pdb=" O   ILE B 276 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   VAL B 278 " --> pdb=" O   ASP B  56 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   ASP B  56 " --> pdb=" O   VAL B 278 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   VAL B 280 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   THR B  54 " --> pdb=" O   VAL B 280 " (cutoff:3.500A)
      removed outlier: 5.632A  pdb=" N   PHE B 282 " --> pdb=" O   PRO B  52 " (cutoff:3.500A)
      removed outlier: 5.675A  pdb=" N   GLU B 295 " --> pdb=" O   GLY B  41 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   THR B  43 " --> pdb=" O   ILE B 293 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ILE B 293 " --> pdb=" O   THR B  43 " (cutoff:3.500A)
      removed outlier: 5.511A  pdb=" N   LYS B  45 " --> pdb=" O   ALA B 291 " (cutoff:3.500A)
      removed outlier: 8.361A  pdb=" N   ALA B 291 " --> pdb=" O   LYS B  45 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   PHE B 315 " --> pdb=" O   ILE B 326 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   ILE B 326 " --> pdb=" O   PHE B 315 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 101 through 102
      removed outlier: 4.583A  pdb=" N   CYS C 392 " --> pdb=" O   ILE C 401 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'B' and resid 123 through 124
    Processing sheet with id=AD2, first strand: chain 'B' and resid 301 through 302
      removed outlier: 3.577A  pdb=" N   PHE B 301 " --> pdb=" O   TRP B 308 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'C' and resid 158 through 162
      removed outlier: 11.364A  pdb=" N   THR C 168 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 7.004A  pdb=" N   ASP C  56 " --> pdb=" O   THR C 168 " (cutoff:3.500A)
      removed outlier: 5.040A  pdb=" N   TYR C 170 " --> pdb=" O   ASP C  56 " (cutoff:3.500A)
      removed outlier: 7.860A  pdb=" N   VAL C 338 " --> pdb=" O   THR C  43 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   LYS C  45 " --> pdb=" O   VAL C 338 " (cutoff:3.500A)
      removed outlier: 7.780A  pdb=" N   CYS C 340 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   LYS C  47 " --> pdb=" O   CYS C 340 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'C' and resid 226 through 227
      removed outlier: 4.244A  pdb=" N   MET C 226 " --> pdb=" O   GLY C 264 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR C 263 " --> pdb=" O   TYR C 281 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   ILE C 277 " --> pdb=" O   ILE C 267 " (cutoff:3.500A)
      removed outlier: 4.865A  pdb=" N   VAL C 269 " --> pdb=" O   TYR C 275 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   TYR C 275 " --> pdb=" O   VAL C 269 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   ILE C 284 " --> pdb=" O   ASN C  51 " (cutoff:3.500A)
      removed outlier: 5.332A  pdb=" N   ASN C  51 " --> pdb=" O   ILE C 284 " (cutoff:3.500A)
      removed outlier: 5.939A  pdb=" N   THR C 286 " --> pdb=" O   LYS C  49 " (cutoff:3.500A)
      removed outlier: 5.543A  pdb=" N   LYS C  49 " --> pdb=" O   THR C 286 " (cutoff:3.500A)
      removed outlier: 5.725A  pdb=" N   GLU C 295 " --> pdb=" O   GLY C  41 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   THR C  43 " --> pdb=" O   ILE C 293 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   ILE C 293 " --> pdb=" O   THR C  43 " (cutoff:3.500A)
      removed outlier: 5.518A  pdb=" N   LYS C  45 " --> pdb=" O   ALA C 291 " (cutoff:3.500A)
      removed outlier: 8.316A  pdb=" N   ALA C 291 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   PHE C 315 " --> pdb=" O   ILE C 326 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   ILE C 326 " --> pdb=" O   PHE C 315 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'C' and resid 301 through 302

    642 hydrogen bonds defined for protein.
    1689 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: 6.01

  Time building geometry restraints manager: 4.49 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 5013
        1.34 -     1.46: 3494
        1.46 -     1.58: 7380
        1.58 -     1.70: 0
        1.70 -     1.83: 102
  Bond restraints: 15989
  Sorted by residual:
  bond pdb=" C1  NAG A 602 "
       pdb=" O5  NAG A 602 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.18e+00
  bond pdb=" CB  VAL G 100 "
       pdb=" CG1 VAL G 100 "
    ideal  model  delta    sigma   weight residual
    1.521  1.475  0.046 3.30e-02 9.18e+02 1.91e+00
  bond pdb=" CA  THR A  88 "
       pdb=" C   THR A  88 "
    ideal  model  delta    sigma   weight residual
    1.520  1.537 -0.017 1.23e-02 6.61e+03 1.91e+00
  bond pdb=" CA  THR C  88 "
       pdb=" C   THR C  88 "
    ideal  model  delta    sigma   weight residual
    1.520  1.536 -0.016 1.23e-02 6.61e+03 1.63e+00
  bond pdb=" CA  THR F  20 "
       pdb=" C   THR F  20 "
    ideal  model  delta    sigma   weight residual
    1.519  1.533 -0.014 1.14e-02 7.69e+03 1.54e+00
  ... (remaining 15984 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 20954
        1.54 -     3.08: 706
        3.08 -     4.62: 76
        4.62 -     6.16: 12
        6.16 -     7.70: 4
  Bond angle restraints: 21752
  Sorted by residual:
  angle pdb=" N   GLU C  95 "
        pdb=" CA  GLU C  95 "
        pdb=" CB  GLU C  95 "
      ideal   model   delta    sigma   weight residual
     110.32  118.02   -7.70 1.70e+00 3.46e-01 2.05e+01
  angle pdb=" CA  GLU C  95 "
        pdb=" CB  GLU C  95 "
        pdb=" CG  GLU C  95 "
      ideal   model   delta    sigma   weight residual
     114.10  120.93   -6.83 2.00e+00 2.50e-01 1.17e+01
  angle pdb=" C   SER D   9 "
        pdb=" N   SER D  10 "
        pdb=" CA  SER D  10 "
      ideal   model   delta    sigma   weight residual
     121.54  127.31   -5.77 1.91e+00 2.74e-01 9.13e+00
  angle pdb=" C   SER A  50 "
        pdb=" N   ASN A  51 "
        pdb=" CA  ASN A  51 "
      ideal   model   delta    sigma   weight residual
     121.80  128.75   -6.95 2.44e+00 1.68e-01 8.12e+00
  angle pdb=" CA  GLY H  50 "
        pdb=" C   GLY H  50 "
        pdb=" N   TYR H  51 "
      ideal   model   delta    sigma   weight residual
     114.48  117.79   -3.31 1.19e+00 7.06e-01 7.75e+00
  ... (remaining 21747 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 9053
       17.97 -    35.94: 562
       35.94 -    53.91: 104
       53.91 -    71.88: 30
       71.88 -    89.85: 14
  Dihedral angle restraints: 9763
    sinusoidal: 3856
      harmonic: 5907
  Sorted by residual:
  dihedral pdb=" CB  CYS C  71 "
           pdb=" SG  CYS C  71 "
           pdb=" SG  CYS C 192 "
           pdb=" CB  CYS C 192 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -147.73   61.73     1      1.00e+01 1.00e-02 5.05e+01
  dihedral pdb=" CB  CYS B  71 "
           pdb=" SG  CYS B  71 "
           pdb=" SG  CYS B 192 "
           pdb=" CB  CYS B 192 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -146.28   60.28     1      1.00e+01 1.00e-02 4.84e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  97 "
           pdb=" CB  CYS H  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  150.10  -57.10     1      1.00e+01 1.00e-02 4.39e+01
  ... (remaining 9760 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1478
       0.033 -    0.066: 694
       0.066 -    0.099: 257
       0.099 -    0.133: 154
       0.133 -    0.166: 19
  Chirality restraints: 2602
  Sorted by residual:
  chirality pdb=" CA  ILE G  38 "
            pdb=" N   ILE G  38 "
            pdb=" C   ILE G  38 "
            pdb=" CB  ILE G  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.87e-01
  chirality pdb=" CA  GLU C  95 "
            pdb=" N   GLU C  95 "
            pdb=" C   GLU C  95 "
            pdb=" CB  GLU C  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.13e-01
  chirality pdb=" CA  VAL A 312 "
            pdb=" N   VAL A 312 "
            pdb=" C   VAL A 312 "
            pdb=" CB  VAL A 312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.15 2.00e-01 2.50e+01 5.99e-01
  ... (remaining 2599 not shown)

  Planarity restraints: 2746
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY I 120 "    0.032 5.00e-02 4.00e+02   4.95e-02 3.91e+00
        pdb=" N   PRO I 121 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO I 121 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO I 121 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN H  62 "   -0.029 5.00e-02 4.00e+02   4.44e-02 3.16e+00
        pdb=" N   PRO H  63 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO H  63 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO H  63 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 446 "   -0.029 5.00e-02 4.00e+02   4.35e-02 3.02e+00
        pdb=" N   PRO B 447 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B 447 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 447 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 2743 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 330
        2.71 -     3.26: 14561
        3.26 -     3.81: 23360
        3.81 -     4.35: 31262
        4.35 -     4.90: 51667
  Nonbonded interactions: 121180
  Sorted by model distance:
  nonbonded pdb=" O   GLY F  30 "
            pdb=" OH  TYR F  71 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" O   GLY E  30 "
            pdb=" OH  TYR E  71 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" NZ  LYS C  60 "
            pdb=" O   ILE C  62 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" O   GLY D  30 "
            pdb=" OH  TYR D  71 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" OG  SER I  36 "
            pdb=" O   GLY I  50 "
     model   vdw
     2.344 3.040
  ... (remaining 121175 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 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'E' and resid 1 through 107)
  selection = (chain 'F' and resid 1 through 107)
}
ncs_group {
  reference = (chain 'G' and resid 1 through 128)
  selection = chain 'H'
  selection = (chain 'I' and resid 1 through 128)
}

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=0.00 max=1.00 mean=0.87
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.650
  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:          0.650
  Check model and map are aligned:         0.090
  Set scattering table:                    0.150
  Process input model:                     39.280
  Find NCS groups from input model:        0.540
  Set up NCS constraints:                  0.070
  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:12.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   61.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
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      :  0.004   0.046  15989  Z= 0.229
  Angle     :  0.663   7.695  21752  Z= 0.379
  Chirality :  0.048   0.166   2602
  Planarity :  0.005   0.049   2740
  Dihedral  : 12.739  89.850   5908
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.18), residues: 2007
  helix:  0.54 (0.25), residues: 420
  sheet:  0.26 (0.23), residues: 534
  loop : -1.12 (0.18), residues: 1053

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP G 106 
 HIS   0.006   0.002   HIS F  34 
 PHE   0.011   0.002   PHE B 212 
 TYR   0.014   0.002   TYR H  51 
 ARG   0.008   0.001   ARG B 375 

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

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

  4014 Ramachandran restraints generated.
    2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4014 Ramachandran restraints generated.
    2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 283
  time to evaluate  : 1.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   37 GLN cc_start: 0.5920 (pp30) cc_final: 0.4241 (pm20)
REVERT: D  107 ARG cc_start: 0.6102 (tmm-80) cc_final: 0.5443 (tpt170)
REVERT: G   53 TYR cc_start: 0.8428 (m-80) cc_final: 0.8044 (m-80)
REVERT: I   38 ILE cc_start: 0.8086 (mt) cc_final: 0.7543 (tt)
REVERT: I   88 THR cc_start: 0.7908 (p) cc_final: 0.7666 (m)
REVERT: I  124 LEU cc_start: 0.7588 (tp) cc_final: 0.7374 (tt)
  outliers start: 0
  outliers final: 1
  residues processed: 283
  average time/residue: 1.5006
  time to fit residues: 463.8561
Evaluate side-chains
  177 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 176
  time to evaluate  : 2.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   46 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 167 optimal weight:    2.9990
   chunk 150 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 101 optimal weight:    5.9990
   chunk 80 optimal weight:    5.9990
   chunk 155 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 115 optimal weight:    1.9990
   chunk 179 optimal weight:    2.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  37 GLN
G  79 GLN
H  79 GLN
I  78 ASN
B 393 GLN
B 395 GLN
C 290 GLN
C 303 ASN
C 393 GLN
C 395 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.095138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.080437 restraints weight = 34377.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 2.52
r_work: 0.3030 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2942
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      339 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2892 r_free = 0.2892    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      274 |
|-----------------------------------------------------------------------------|
r_final: 0.2892
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045  15989  Z= 0.457
  Angle     :  0.708   8.279  21752  Z= 0.384
  Chirality :  0.052   0.172   2602
  Planarity :  0.006   0.052   2740
  Dihedral  :  5.289  34.549   2294
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  :  8.59 %
    Favored  : 88.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.18), residues: 2007
  helix:  1.23 (0.26), residues: 405
  sheet:  0.25 (0.21), residues: 568
  loop : -1.13 (0.18), residues: 1034

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP G 106 
 HIS   0.005   0.002   HIS A  29 
 PHE   0.017   0.002   PHE C 212 
 TYR   0.020   0.002   TYR H  33 
 ARG   0.006   0.001   ARG F  50 

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

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

  4014 Ramachandran restraints generated.
    2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4014 Ramachandran restraints generated.
    2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 184
  time to evaluate  : 1.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.6808 (mpt)
REVERT: D   36 TYR cc_start: 0.8915 (m-80) cc_final: 0.8567 (m-80)
REVERT: D  107 ARG cc_start: 0.6623 (tmm-80) cc_final: 0.5351 (tpm170)
REVERT: E   82 ASP cc_start: 0.7907 (p0) cc_final: 0.7219 (p0)
REVERT: G   34 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.7914 (ptt-90)
REVERT: H   47 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.8976 (tt0)
REVERT: I   38 ILE cc_start: 0.9044 (mt) cc_final: 0.7929 (tt)
REVERT: I   39 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7876 (ppt-90)
REVERT: I   77 LYS cc_start: 0.7493 (tmtm) cc_final: 0.7082 (ptmm)
REVERT: B  102 HIS cc_start: 0.7495 (p90) cc_final: 0.7230 (p-80)
REVERT: B  290 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8288 (mp10)
REVERT: C   61 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.7063 (mpt)
REVERT: C  290 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8835 (mt0)
  outliers start: 51
  outliers final: 17
  residues processed: 215
  average time/residue: 1.4295
  time to fit residues: 338.3224
Evaluate side-chains
  189 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 165
  time to evaluate  : 2.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain E residue   37 GLN
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain G residue   34 ARG
Chi-restraints excluded: chain G residue   70 THR
Chi-restraints excluded: chain G residue   75 THR
Chi-restraints excluded: chain G residue  126 THR
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   47 GLU
Chi-restraints excluded: chain H residue   68 ARG
Chi-restraints excluded: chain I residue   39 ARG
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  290 GLN
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  348 MET
Chi-restraints excluded: chain C residue   61 MET
Chi-restraints excluded: chain C residue  290 GLN
Chi-restraints excluded: chain C residue  309 ILE
Chi-restraints excluded: chain C residue  335 LYS
Chi-restraints excluded: chain C residue  449 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 152 optimal weight:    1.9990
   chunk 166 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 69 optimal weight:    5.9990
   chunk 87 optimal weight:    0.0060
   chunk 29 optimal weight:    0.5980
   chunk 112 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 110 optimal weight:    0.7980
   chunk 47 optimal weight:    8.9990
   chunk 86 optimal weight:    0.7980
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 303 ASN
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  37 GLN
** E  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  83 ASN
H  60 ASN
I  40 GLN
B 182 ASN
B 393 GLN
B 395 GLN
C 290 GLN
C 395 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.099675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.084163 restraints weight = 33957.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 2.52
r_work: 0.3031 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2955
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      274 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2958 r_free = 0.2958    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      343 |
|-----------------------------------------------------------------------------|
r_final: 0.2958
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15989  Z= 0.180
  Angle     :  0.553   9.914  21752  Z= 0.294
  Chirality :  0.046   0.147   2602
  Planarity :  0.005   0.045   2740
  Dihedral  :  4.570  20.170   2292
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 11.27 %
    Favored  : 86.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.18), residues: 2007
  helix:  1.69 (0.26), residues: 408
  sheet:  0.43 (0.22), residues: 572
  loop : -1.00 (0.18), residues: 1027

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP G 106 
 HIS   0.003   0.001   HIS B 102 
 PHE   0.010   0.001   PHE B 301 
 TYR   0.018   0.001   TYR H  33 
 ARG   0.005   0.000   ARG C 336 

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

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

  4014 Ramachandran restraints generated.
    2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4014 Ramachandran restraints generated.
    2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 189
  time to evaluate  : 2.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.6574 (mpt)
REVERT: D   22 THR cc_start: 0.7178 (p) cc_final: 0.6710 (m)
REVERT: D   79 GLN cc_start: 0.8172 (mm110) cc_final: 0.7971 (mm-40)
REVERT: D   88 GLN cc_start: 0.8418 (tt0) cc_final: 0.8201 (tt0)
REVERT: D  107 ARG cc_start: 0.6519 (tmm-80) cc_final: 0.5648 (tpm170)
REVERT: E   37 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.6920 (tt0)
REVERT: E   82 ASP cc_start: 0.7594 (p0) cc_final: 0.6447 (p0)
REVERT: E  101 THR cc_start: 0.7706 (t) cc_final: 0.7327 (p)
REVERT: E  105 ILE cc_start: 0.4183 (mp) cc_final: 0.2039 (tp)
REVERT: H   91 ASP cc_start: 0.8502 (m-30) cc_final: 0.7786 (m-30)
REVERT: I   38 ILE cc_start: 0.9078 (mt) cc_final: 0.7941 (tt)
REVERT: I   77 LYS cc_start: 0.7150 (tmtm) cc_final: 0.6879 (ptmm)
REVERT: B  102 HIS cc_start: 0.7286 (p90) cc_final: 0.7009 (p-80)
REVERT: B  244 ARG cc_start: 0.8230 (ttm110) cc_final: 0.7997 (ttp80)
REVERT: B  290 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8140 (mp10)
REVERT: B  304 ASP cc_start: 0.8257 (t0) cc_final: 0.8028 (t0)
REVERT: B  449 VAL cc_start: 0.6862 (m) cc_final: 0.6545 (p)
REVERT: C   61 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8656 (mmm)
REVERT: C  152 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8401 (tm-30)
  outliers start: 39
  outliers final: 10
  residues processed: 211
  average time/residue: 1.4100
  time to fit residues: 327.6214
Evaluate side-chains
  192 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 178
  time to evaluate  : 1.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain E residue   37 GLN
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain I residue   51 TYR
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  290 GLN
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue   61 MET
Chi-restraints excluded: chain C residue  309 ILE
Chi-restraints excluded: chain C residue  449 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 103 optimal weight:    0.9990
   chunk 171 optimal weight:    3.9990
   chunk 96 optimal weight:    0.7980
   chunk 11 optimal weight:    0.1980
   chunk 166 optimal weight:    0.9980
   chunk 184 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 150 optimal weight:    0.9990
   chunk 169 optimal weight:    3.9990
   chunk 172 optimal weight:    0.9980
   chunk 192 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 102 HIS
** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  31 ASN
E  37 GLN
H  78 ASN
H  79 GLN
I  40 GLN
C 395 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.094858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.078390 restraints weight = 34271.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 2.57
r_work: 0.3041 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2952
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2952 r_free = 0.2952    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      343 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2954 r_free = 0.2954    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      350 |
|-----------------------------------------------------------------------------|
r_final: 0.2954
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15989  Z= 0.194
  Angle     :  0.550  11.068  21752  Z= 0.289
  Chirality :  0.046   0.145   2602
  Planarity :  0.004   0.044   2740
  Dihedral  :  4.361  20.204   2292
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 12.27 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.19), residues: 2007
  helix:  1.93 (0.26), residues: 408
  sheet:  0.53 (0.22), residues: 548
  loop : -0.98 (0.18), residues: 1051

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP G 106 
 HIS   0.005   0.001   HIS A 102 
 PHE   0.011   0.001   PHE B 301 
 TYR   0.055   0.001   TYR I  51 
 ARG   0.005   0.000   ARG C 336 

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

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

  4014 Ramachandran restraints generated.
    2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4014 Ramachandran restraints generated.
    2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 187
  time to evaluate  : 1.797 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.6504 (mpt)
REVERT: A   95 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8612 (mt-10)
REVERT: A  166 GLU cc_start: 0.8622 (pm20) cc_final: 0.8361 (pp20)
REVERT: D   22 THR cc_start: 0.7201 (p) cc_final: 0.6745 (m)
REVERT: D   37 GLN cc_start: 0.7182 (pp30) cc_final: 0.6913 (pm20)
REVERT: D   79 GLN cc_start: 0.8292 (mm110) cc_final: 0.8081 (mm-40)
REVERT: D   86 TYR cc_start: 0.7967 (m-80) cc_final: 0.7049 (m-80)
REVERT: D  103 VAL cc_start: 0.5865 (t) cc_final: 0.5551 (p)
REVERT: D  107 ARG cc_start: 0.6826 (tmm-80) cc_final: 0.5719 (tpm170)
REVERT: E   11 LEU cc_start: 0.8305 (tm) cc_final: 0.7933 (tt)
REVERT: E   37 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.6867 (tt0)
REVERT: E   82 ASP cc_start: 0.7561 (p0) cc_final: 0.6361 (p0)
REVERT: E   88 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8668 (tm130)
REVERT: E  101 THR cc_start: 0.7719 (t) cc_final: 0.7299 (p)
REVERT: E  105 ILE cc_start: 0.4179 (mp) cc_final: 0.2151 (tp)
REVERT: H   47 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8736 (tt0)
REVERT: H   83 ASN cc_start: 0.9329 (t0) cc_final: 0.8914 (m110)
REVERT: H   91 ASP cc_start: 0.8492 (m-30) cc_final: 0.7896 (m-30)
REVERT: I   38 ILE cc_start: 0.9029 (mt) cc_final: 0.7887 (tt)
REVERT: I  117 ASP cc_start: 0.8410 (p0) cc_final: 0.8083 (p0)
REVERT: B  102 HIS cc_start: 0.7180 (p90) cc_final: 0.6897 (p-80)
REVERT: B  244 ARG cc_start: 0.8231 (ttm110) cc_final: 0.8000 (ttp80)
REVERT: B  290 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8138 (mp10)
REVERT: B  304 ASP cc_start: 0.8315 (t0) cc_final: 0.8039 (t0)
REVERT: B  449 VAL cc_start: 0.6846 (m) cc_final: 0.6548 (p)
REVERT: C   61 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8700 (mmm)
REVERT: C  449 VAL cc_start: 0.7155 (OUTLIER) cc_final: 0.6642 (p)
  outliers start: 38
  outliers final: 14
  residues processed: 207
  average time/residue: 1.4451
  time to fit residues: 330.3093
Evaluate side-chains
  195 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 174
  time to evaluate  : 1.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain E residue   20 THR
Chi-restraints excluded: chain E residue   37 GLN
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   88 GLN
Chi-restraints excluded: chain G residue   75 THR
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain H residue   47 GLU
Chi-restraints excluded: chain H residue   68 ARG
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  290 GLN
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  348 MET
Chi-restraints excluded: chain C residue   61 MET
Chi-restraints excluded: chain C residue  138 MET
Chi-restraints excluded: chain C residue  309 ILE
Chi-restraints excluded: chain C residue  449 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 147 optimal weight:    2.9990
   chunk 188 optimal weight:    3.9990
   chunk 127 optimal weight:    1.9990
   chunk 123 optimal weight:    1.9990
   chunk 172 optimal weight:    2.9990
   chunk 178 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 94 optimal weight:    7.9990
   chunk 156 optimal weight:    0.8980
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  31 ASN
E  37 GLN
I  60 ASN
C 395 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.094442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.077519 restraints weight = 34668.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 2.59
r_work: 0.2987 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2897
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      350 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2896 r_free = 0.2896    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      356 |
|-----------------------------------------------------------------------------|
r_final: 0.2896
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  15989  Z= 0.354
  Angle     :  0.628   9.597  21752  Z= 0.336
  Chirality :  0.049   0.207   2602
  Planarity :  0.005   0.047   2740
  Dihedral  :  4.731  21.024   2292
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 12.77 %
    Favored  : 84.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.18), residues: 2007
  helix:  1.70 (0.26), residues: 408
  sheet:  0.41 (0.22), residues: 558
  loop : -1.05 (0.18), residues: 1041

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP G 106 
 HIS   0.005   0.002   HIS F  34 
 PHE   0.017   0.002   PHE I  80 
 TYR   0.018   0.002   TYR I  33 
 ARG   0.007   0.001   ARG C 336 

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

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

  4014 Ramachandran restraints generated.
    2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4014 Ramachandran restraints generated.
    2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 175
  time to evaluate  : 2.012 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.6756 (mpt)
REVERT: A   95 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8682 (mt-10)
REVERT: A  164 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7832 (p)
REVERT: A  327 GLU cc_start: 0.9072 (mp0) cc_final: 0.8849 (mp0)
REVERT: D   22 THR cc_start: 0.7397 (p) cc_final: 0.7032 (m)
REVERT: D   79 GLN cc_start: 0.8308 (mm110) cc_final: 0.7937 (mm110)
REVERT: D   86 TYR cc_start: 0.8049 (m-80) cc_final: 0.7098 (m-80)
REVERT: D  107 ARG cc_start: 0.6888 (tmm-80) cc_final: 0.5721 (tpm170)
REVERT: E   37 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.6931 (tt0)
REVERT: E   82 ASP cc_start: 0.7384 (p0) cc_final: 0.6091 (p0)
REVERT: E   88 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8767 (tm-30)
REVERT: E  105 ILE cc_start: 0.4359 (mp) cc_final: 0.2393 (tp)
REVERT: H   47 GLU cc_start: 0.9157 (OUTLIER) cc_final: 0.8722 (tt0)
REVERT: H   74 ASP cc_start: 0.8316 (t0) cc_final: 0.8037 (t0)
REVERT: I   38 ILE cc_start: 0.9136 (mt) cc_final: 0.8013 (tt)
REVERT: I  117 ASP cc_start: 0.8385 (p0) cc_final: 0.8094 (p0)
REVERT: B  102 HIS cc_start: 0.7436 (p90) cc_final: 0.7152 (p-80)
REVERT: B  290 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8250 (mp10)
REVERT: B  304 ASP cc_start: 0.8438 (t0) cc_final: 0.8158 (t0)
REVERT: B  449 VAL cc_start: 0.6888 (m) cc_final: 0.6570 (p)
REVERT: C   61 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.7040 (mpt)
REVERT: C  327 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8320 (mp0)
  outliers start: 47
  outliers final: 24
  residues processed: 202
  average time/residue: 1.4670
  time to fit residues: 325.6334
Evaluate side-chains
  201 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 170
  time to evaluate  : 1.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain E residue   20 THR
Chi-restraints excluded: chain E residue   37 GLN
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   88 GLN
Chi-restraints excluded: chain F residue   11 LEU
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain G residue   75 THR
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain H residue   47 GLU
Chi-restraints excluded: chain H residue   68 ARG
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  290 GLN
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  348 MET
Chi-restraints excluded: chain C residue   61 MET
Chi-restraints excluded: chain C residue  115 MET
Chi-restraints excluded: chain C residue  152 GLU
Chi-restraints excluded: chain C residue  219 GLN
Chi-restraints excluded: chain C residue  309 ILE
Chi-restraints excluded: chain C residue  335 LYS
Chi-restraints excluded: chain C residue  449 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 154 optimal weight:    0.8980
   chunk 125 optimal weight:    4.9990
   chunk 47 optimal weight:    4.9990
   chunk 150 optimal weight:    0.9990
   chunk 157 optimal weight:    0.8980
   chunk 170 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 178 optimal weight:    0.5980
   chunk 51 optimal weight:    5.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  31 ASN
E  37 GLN
** I  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 395 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.096115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.078866 restraints weight = 34045.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 2.58
r_work: 0.3016 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2924
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2924 r_free = 0.2924    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      356 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      374 |
|-----------------------------------------------------------------------------|
r_final: 0.2923
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15989  Z= 0.213
  Angle     :  0.567   9.840  21752  Z= 0.299
  Chirality :  0.046   0.183   2602
  Planarity :  0.004   0.044   2740
  Dihedral  :  4.470  20.340   2292
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 13.78 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.00 (0.18), residues: 2007
  helix:  1.84 (0.26), residues: 408
  sheet:  0.46 (0.22), residues: 558
  loop : -1.04 (0.18), residues: 1041

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP G 106 
 HIS   0.004   0.001   HIS F  34 
 PHE   0.014   0.001   PHE I  80 
 TYR   0.020   0.001   TYR D  49 
 ARG   0.006   0.000   ARG C 336 

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

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

  4014 Ramachandran restraints generated.
    2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4014 Ramachandran restraints generated.
    2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 175
  time to evaluate  : 1.863 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.6715 (mpt)
REVERT: A   95 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8637 (mt-10)
REVERT: A  164 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7780 (p)
REVERT: A  327 GLU cc_start: 0.9060 (mp0) cc_final: 0.8858 (mp0)
REVERT: D   22 THR cc_start: 0.7316 (p) cc_final: 0.6981 (m)
REVERT: D   37 GLN cc_start: 0.7163 (pp30) cc_final: 0.6464 (pm20)
REVERT: D   86 TYR cc_start: 0.8070 (m-80) cc_final: 0.7215 (m-80)
REVERT: D  107 ARG cc_start: 0.6766 (tmm-80) cc_final: 0.5736 (tpm170)
REVERT: E   37 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6554 (tt0)
REVERT: E   82 ASP cc_start: 0.7447 (p0) cc_final: 0.6099 (p0)
REVERT: E   88 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8481 (tm-30)
REVERT: E  105 ILE cc_start: 0.4372 (mp) cc_final: 0.2419 (tp)
REVERT: H   47 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8647 (tt0)
REVERT: H   83 ASN cc_start: 0.9301 (t0) cc_final: 0.8801 (m-40)
REVERT: H   91 ASP cc_start: 0.8555 (m-30) cc_final: 0.8082 (m-30)
REVERT: I   38 ILE cc_start: 0.9097 (mt) cc_final: 0.7993 (tt)
REVERT: I   39 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7678 (ptt90)
REVERT: I  117 ASP cc_start: 0.8326 (p0) cc_final: 0.8045 (p0)
REVERT: B  102 HIS cc_start: 0.7365 (p90) cc_final: 0.7100 (p-80)
REVERT: B  290 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8228 (mp10)
REVERT: B  304 ASP cc_start: 0.8424 (t0) cc_final: 0.8140 (t0)
REVERT: B  449 VAL cc_start: 0.6931 (m) cc_final: 0.6633 (p)
REVERT: C   61 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.6896 (mpt)
REVERT: C  327 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8600 (mp0)
  outliers start: 44
  outliers final: 19
  residues processed: 198
  average time/residue: 1.4445
  time to fit residues: 314.9736
Evaluate side-chains
  196 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 169
  time to evaluate  : 1.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  115 MET
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain E residue   20 THR
Chi-restraints excluded: chain E residue   37 GLN
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   88 GLN
Chi-restraints excluded: chain E residue  103 VAL
Chi-restraints excluded: chain F residue   11 LEU
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain G residue   75 THR
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain H residue   47 GLU
Chi-restraints excluded: chain H residue   68 ARG
Chi-restraints excluded: chain I residue   39 ARG
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  290 GLN
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  348 MET
Chi-restraints excluded: chain C residue   61 MET
Chi-restraints excluded: chain C residue  152 GLU
Chi-restraints excluded: chain C residue  309 ILE
Chi-restraints excluded: chain C residue  449 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 115 optimal weight:    0.5980
   chunk 35 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9980
   chunk 104 optimal weight:    5.9990
   chunk 161 optimal weight:    1.9990
   chunk 173 optimal weight:    2.9990
   chunk 113 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 148 optimal weight:    0.8980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  31 ASN
E  37 GLN
C 395 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.095299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.077824 restraints weight = 34195.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 2.59
r_work: 0.3000 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2913 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2910
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      374 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      374 |
|-----------------------------------------------------------------------------|
r_final: 0.2910
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  15989  Z= 0.273
  Angle     :  0.591   9.097  21752  Z= 0.313
  Chirality :  0.047   0.193   2602
  Planarity :  0.005   0.045   2740
  Dihedral  :  4.536  20.648   2292
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 13.66 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.18), residues: 2007
  helix:  1.83 (0.26), residues: 408
  sheet:  0.52 (0.22), residues: 550
  loop : -1.08 (0.18), residues: 1049

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP G 106 
 HIS   0.005   0.001   HIS F  34 
 PHE   0.013   0.002   PHE I  80 
 TYR   0.021   0.002   TYR D  49 
 ARG   0.007   0.001   ARG C 336 

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

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

  4014 Ramachandran restraints generated.
    2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4014 Ramachandran restraints generated.
    2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 171
  time to evaluate  : 2.032 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.6711 (mpt)
REVERT: A   95 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8641 (mt-10)
REVERT: A  164 THR cc_start: 0.8101 (OUTLIER) cc_final: 0.7813 (p)
REVERT: A  327 GLU cc_start: 0.9077 (mp0) cc_final: 0.8843 (mp0)
REVERT: D   22 THR cc_start: 0.7299 (p) cc_final: 0.7033 (m)
REVERT: D   37 GLN cc_start: 0.7337 (pp30) cc_final: 0.6935 (pm20)
REVERT: D   86 TYR cc_start: 0.8054 (m-80) cc_final: 0.7309 (m-80)
REVERT: D  107 ARG cc_start: 0.6801 (tmm-80) cc_final: 0.5681 (tpm170)
REVERT: E   37 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.6732 (tt0)
REVERT: E   82 ASP cc_start: 0.7401 (p0) cc_final: 0.6483 (p0)
REVERT: E   88 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8406 (tm-30)
REVERT: H   47 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8665 (tt0)
REVERT: H   74 ASP cc_start: 0.8543 (t0) cc_final: 0.8252 (t0)
REVERT: H   83 ASN cc_start: 0.9256 (t0) cc_final: 0.8756 (m-40)
REVERT: H   91 ASP cc_start: 0.8547 (m-30) cc_final: 0.8226 (m-30)
REVERT: I   21 THR cc_start: 0.9078 (p) cc_final: 0.8822 (t)
REVERT: I   38 ILE cc_start: 0.9102 (mt) cc_final: 0.8009 (tt)
REVERT: I   39 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7607 (ptt90)
REVERT: I  117 ASP cc_start: 0.8434 (p0) cc_final: 0.8207 (p0)
REVERT: B  102 HIS cc_start: 0.7413 (p90) cc_final: 0.7137 (p-80)
REVERT: B  219 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8624 (pt0)
REVERT: B  290 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8259 (mp10)
REVERT: B  304 ASP cc_start: 0.8473 (t0) cc_final: 0.8212 (t0)
REVERT: B  449 VAL cc_start: 0.6958 (m) cc_final: 0.6644 (p)
REVERT: C   61 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.6925 (mpt)
REVERT: C  327 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8621 (mp0)
  outliers start: 53
  outliers final: 27
  residues processed: 204
  average time/residue: 1.4083
  time to fit residues: 316.2206
Evaluate side-chains
  203 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 167
  time to evaluate  : 2.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   65 SER
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain E residue   20 THR
Chi-restraints excluded: chain E residue   37 GLN
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   88 GLN
Chi-restraints excluded: chain E residue  103 VAL
Chi-restraints excluded: chain F residue   11 LEU
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   78 LEU
Chi-restraints excluded: chain G residue   70 THR
Chi-restraints excluded: chain G residue   75 THR
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain H residue   21 THR
Chi-restraints excluded: chain H residue   47 GLU
Chi-restraints excluded: chain H residue   68 ARG
Chi-restraints excluded: chain I residue   39 ARG
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  219 GLN
Chi-restraints excluded: chain B residue  290 GLN
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  335 LYS
Chi-restraints excluded: chain B residue  348 MET
Chi-restraints excluded: chain C residue   61 MET
Chi-restraints excluded: chain C residue  115 MET
Chi-restraints excluded: chain C residue  152 GLU
Chi-restraints excluded: chain C residue  309 ILE
Chi-restraints excluded: chain C residue  449 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 169 optimal weight:    0.9990
   chunk 88 optimal weight:    6.9990
   chunk 135 optimal weight:    0.9980
   chunk 151 optimal weight:    0.7980
   chunk 153 optimal weight:    0.3980
   chunk 66 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 85 optimal weight:    0.8980
   chunk 186 optimal weight:    0.6980
   chunk 90 optimal weight:    1.9990
   chunk 180 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 290 GLN
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  31 ASN
E  37 GLN
C 395 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.096687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.078822 restraints weight = 33950.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 2.60
r_work: 0.3025 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2934
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2934 r_free = 0.2934    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      374 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2934 r_free = 0.2934    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      379 |
|-----------------------------------------------------------------------------|
r_final: 0.2934
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.2701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15989  Z= 0.192
  Angle     :  0.561   8.924  21752  Z= 0.296
  Chirality :  0.046   0.185   2602
  Planarity :  0.004   0.043   2740
  Dihedral  :  4.351  20.064   2292
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 14.17 %
    Favored  : 82.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.19), residues: 2007
  helix:  1.99 (0.26), residues: 408
  sheet:  0.58 (0.22), residues: 550
  loop : -1.03 (0.18), residues: 1049

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP G 106 
 HIS   0.003   0.001   HIS F  34 
 PHE   0.023   0.001   PHE I  80 
 TYR   0.021   0.001   TYR D  49 
 ARG   0.007   0.000   ARG C 336 

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

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

  4014 Ramachandran restraints generated.
    2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4014 Ramachandran restraints generated.
    2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 176
  time to evaluate  : 1.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.6662 (mpt)
REVERT: A   70 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7745 (pm20)
REVERT: A   95 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8592 (mt-10)
REVERT: A  164 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7866 (p)
REVERT: D   37 GLN cc_start: 0.7498 (pp30) cc_final: 0.7118 (pm20)
REVERT: D   58 ILE cc_start: 0.8069 (mm) cc_final: 0.7836 (mm)
REVERT: D   86 TYR cc_start: 0.8079 (m-80) cc_final: 0.7346 (m-80)
REVERT: D  107 ARG cc_start: 0.6645 (tmm-80) cc_final: 0.5569 (tpm170)
REVERT: E   37 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6510 (tt0)
REVERT: E   82 ASP cc_start: 0.7436 (p0) cc_final: 0.6324 (p0)
REVERT: E   88 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8409 (tm-30)
REVERT: H   83 ASN cc_start: 0.9249 (t0) cc_final: 0.8748 (m-40)
REVERT: H   91 ASP cc_start: 0.8489 (m-30) cc_final: 0.8208 (m-30)
REVERT: I   38 ILE cc_start: 0.9053 (mt) cc_final: 0.7979 (tt)
REVERT: I   39 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7568 (ptt90)
REVERT: I  117 ASP cc_start: 0.8398 (p0) cc_final: 0.8148 (p0)
REVERT: B   68 MET cc_start: 0.8050 (ptm) cc_final: 0.7733 (ptp)
REVERT: B  102 HIS cc_start: 0.7344 (p90) cc_final: 0.7081 (p-80)
REVERT: B  103 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8330 (m-30)
REVERT: B  290 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8195 (mp10)
REVERT: B  304 ASP cc_start: 0.8474 (t0) cc_final: 0.8204 (t0)
REVERT: B  449 VAL cc_start: 0.6938 (m) cc_final: 0.6662 (p)
REVERT: C   61 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8712 (mmm)
REVERT: C  327 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8421 (mp0)
  outliers start: 52
  outliers final: 26
  residues processed: 207
  average time/residue: 1.4002
  time to fit residues: 319.3272
Evaluate side-chains
  202 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 167
  time to evaluate  : 2.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   65 SER
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain E residue   20 THR
Chi-restraints excluded: chain E residue   37 GLN
Chi-restraints excluded: chain E residue   73 LEU
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   88 GLN
Chi-restraints excluded: chain F residue   11 LEU
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   78 LEU
Chi-restraints excluded: chain G residue   75 THR
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain H residue   21 THR
Chi-restraints excluded: chain H residue   68 ARG
Chi-restraints excluded: chain I residue   39 ARG
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  103 ASP
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  290 GLN
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  335 LYS
Chi-restraints excluded: chain B residue  348 MET
Chi-restraints excluded: chain C residue   61 MET
Chi-restraints excluded: chain C residue  309 ILE
Chi-restraints excluded: chain C residue  449 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 189 optimal weight:    2.9990
   chunk 132 optimal weight:    1.9990
   chunk 140 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   chunk 124 optimal weight:    0.0270
   chunk 113 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   chunk 190 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.8440

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

Flipped N/Q/H residues before XYZ refinement:
A 290 GLN
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  37 GLN
C 395 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.096759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.078590 restraints weight = 33965.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 2.61
r_work: 0.3020 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2932 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2932
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      379 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      382 |
|-----------------------------------------------------------------------------|
r_final: 0.2931
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15989  Z= 0.210
  Angle     :  0.566   8.848  21752  Z= 0.298
  Chirality :  0.046   0.175   2602
  Planarity :  0.004   0.043   2740
  Dihedral  :  4.324  20.089   2292
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 14.72 %
    Favored  : 82.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.19), residues: 2007
  helix:  2.02 (0.26), residues: 408
  sheet:  0.63 (0.22), residues: 544
  loop : -1.04 (0.18), residues: 1055

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP G 106 
 HIS   0.004   0.001   HIS F  34 
 PHE   0.023   0.001   PHE I  80 
 TYR   0.021   0.001   TYR D  49 
 ARG   0.007   0.001   ARG C 336 

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

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

  4014 Ramachandran restraints generated.
    2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4014 Ramachandran restraints generated.
    2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 167
  time to evaluate  : 1.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.6630 (mpt)
REVERT: A   70 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7738 (pm20)
REVERT: A   95 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8595 (mt-10)
REVERT: A  164 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7880 (p)
REVERT: D   22 THR cc_start: 0.7199 (p) cc_final: 0.6996 (m)
REVERT: D   86 TYR cc_start: 0.8064 (m-80) cc_final: 0.7366 (m-80)
REVERT: D  107 ARG cc_start: 0.6569 (tmm-80) cc_final: 0.5559 (tpm170)
REVERT: E   37 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.6356 (OUTLIER)
REVERT: E   45 LYS cc_start: 0.8942 (ptmt) cc_final: 0.8656 (ptmm)
REVERT: E   82 ASP cc_start: 0.7304 (p0) cc_final: 0.6404 (p0)
REVERT: E   88 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8389 (tm-30)
REVERT: F   17 ASP cc_start: 0.8844 (m-30) cc_final: 0.8621 (m-30)
REVERT: H   47 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8658 (tt0)
REVERT: H   83 ASN cc_start: 0.9224 (t0) cc_final: 0.8720 (m-40)
REVERT: H   91 ASP cc_start: 0.8415 (m-30) cc_final: 0.8209 (m-30)
REVERT: I   38 ILE cc_start: 0.9039 (mt) cc_final: 0.7979 (tt)
REVERT: I   39 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7541 (ptt90)
REVERT: I  117 ASP cc_start: 0.8396 (p0) cc_final: 0.8168 (p0)
REVERT: B  102 HIS cc_start: 0.7314 (p90) cc_final: 0.7053 (p-80)
REVERT: B  103 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8350 (m-30)
REVERT: B  152 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7818 (pp20)
REVERT: B  290 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8177 (mp10)
REVERT: B  304 ASP cc_start: 0.8493 (t0) cc_final: 0.8226 (t0)
REVERT: B  449 VAL cc_start: 0.6879 (m) cc_final: 0.6615 (p)
REVERT: C   61 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8722 (mmm)
REVERT: C  327 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8577 (mp0)
  outliers start: 44
  outliers final: 27
  residues processed: 193
  average time/residue: 1.4495
  time to fit residues: 307.7969
Evaluate side-chains
  201 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 165
  time to evaluate  : 1.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   65 SER
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain E residue   20 THR
Chi-restraints excluded: chain E residue   33 LEU
Chi-restraints excluded: chain E residue   37 GLN
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   88 GLN
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain G residue   75 THR
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain H residue   21 THR
Chi-restraints excluded: chain H residue   47 GLU
Chi-restraints excluded: chain H residue   68 ARG
Chi-restraints excluded: chain H residue   74 ASP
Chi-restraints excluded: chain I residue   39 ARG
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  103 ASP
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  290 GLN
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  335 LYS
Chi-restraints excluded: chain B residue  348 MET
Chi-restraints excluded: chain C residue   61 MET
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  309 ILE
Chi-restraints excluded: chain C residue  449 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 60 optimal weight:    0.0000
   chunk 134 optimal weight:    0.8980
   chunk 78 optimal weight:    0.0970
   chunk 189 optimal weight:    0.9990
   chunk 196 optimal weight:    4.9990
   chunk 191 optimal weight:    0.7980
   chunk 140 optimal weight:    0.7980
   chunk 104 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 192 optimal weight:    0.9990
   overall best weight:    0.5182

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

Flipped N/Q/H residues before XYZ refinement:
A 290 GLN
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  37 GLN
** I  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 395 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.097727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.079369 restraints weight = 34179.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 2.62
r_work: 0.3040 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2951
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2951 r_free = 0.2951    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      382 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2950 r_free = 0.2950    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      395 |
|-----------------------------------------------------------------------------|
r_final: 0.2950
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.2827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  15989  Z= 0.176
  Angle     :  0.568  12.900  21752  Z= 0.296
  Chirality :  0.045   0.174   2602
  Planarity :  0.004   0.042   2740
  Dihedral  :  4.216  19.840   2292
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.11 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.19), residues: 2007
  helix:  2.14 (0.26), residues: 408
  sheet:  0.60 (0.22), residues: 563
  loop : -0.98 (0.18), residues: 1036

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP G 106 
 HIS   0.003   0.001   HIS E  34 
 PHE   0.022   0.001   PHE I  80 
 TYR   0.022   0.001   TYR D  49 
 ARG   0.007   0.001   ARG C 336 

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

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

  4014 Ramachandran restraints generated.
    2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4014 Ramachandran restraints generated.
    2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 168
  time to evaluate  : 1.873 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.6607 (mpt)
REVERT: A   70 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7724 (pm20)
REVERT: A   95 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8588 (mt-10)
REVERT: A  164 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7903 (p)
REVERT: D   37 GLN cc_start: 0.7235 (pp30) cc_final: 0.6139 (pm20)
REVERT: D   86 TYR cc_start: 0.8050 (m-80) cc_final: 0.7312 (m-80)
REVERT: D  107 ARG cc_start: 0.6566 (tmm-80) cc_final: 0.5516 (tpm170)
REVERT: E   37 GLN cc_start: 0.6677 (OUTLIER) cc_final: 0.6005 (tm-30)
REVERT: E   61 ARG cc_start: 0.8730 (mtm-85) cc_final: 0.8122 (ttp-110)
REVERT: E   88 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8382 (tm-30)
REVERT: F   17 ASP cc_start: 0.8854 (m-30) cc_final: 0.8598 (m-30)
REVERT: F   72 THR cc_start: 0.9553 (t) cc_final: 0.9280 (p)
REVERT: H   83 ASN cc_start: 0.9192 (t0) cc_final: 0.8703 (m-40)
REVERT: H   91 ASP cc_start: 0.8412 (m-30) cc_final: 0.8188 (m-30)
REVERT: I   38 ILE cc_start: 0.9013 (mt) cc_final: 0.7952 (tt)
REVERT: I   39 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7510 (ptt90)
REVERT: I  117 ASP cc_start: 0.8424 (p0) cc_final: 0.8221 (p0)
REVERT: B   68 MET cc_start: 0.7899 (ptm) cc_final: 0.7628 (ptp)
REVERT: B  102 HIS cc_start: 0.7223 (p90) cc_final: 0.6968 (p-80)
REVERT: B  103 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8301 (m-30)
REVERT: B  152 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7807 (pp20)
REVERT: B  304 ASP cc_start: 0.8493 (t0) cc_final: 0.8237 (t0)
REVERT: B  449 VAL cc_start: 0.6905 (m) cc_final: 0.6648 (p)
REVERT: C   61 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8691 (mmm)
REVERT: C  327 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8598 (mp0)
REVERT: C  449 VAL cc_start: 0.7187 (OUTLIER) cc_final: 0.6644 (p)
  outliers start: 38
  outliers final: 21
  residues processed: 193
  average time/residue: 1.4681
  time to fit residues: 313.3612
Evaluate side-chains
  195 residues out of total 1793 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 165
  time to evaluate  : 1.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  309 ILE
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain D residue   33 LEU
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain E residue   20 THR
Chi-restraints excluded: chain E residue   37 GLN
Chi-restraints excluded: chain E residue   74 THR
Chi-restraints excluded: chain E residue   88 GLN
Chi-restraints excluded: chain F residue   19 VAL
Chi-restraints excluded: chain F residue   78 LEU
Chi-restraints excluded: chain G residue   75 THR
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain H residue   68 ARG
Chi-restraints excluded: chain H residue   74 ASP
Chi-restraints excluded: chain I residue   39 ARG
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  103 ASP
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  348 MET
Chi-restraints excluded: chain C residue   61 MET
Chi-restraints excluded: chain C residue  211 LEU
Chi-restraints excluded: chain C residue  449 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 190 optimal weight:    3.9990
   chunk 148 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 113 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0670
   chunk 71 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 135 optimal weight:    1.9990
   chunk 153 optimal weight:    2.9990
   chunk 109 optimal weight:    0.7980
   chunk 124 optimal weight:    0.0870
   overall best weight:    0.7698

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

Flipped N/Q/H residues before XYZ refinement:
A 290 GLN
** D  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  37 GLN
** I  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 395 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.097545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.078999 restraints weight = 34047.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 2.62
r_work: 0.3031 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2943 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2940
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      395 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2940 r_free = 0.2940    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:      399 |
|-----------------------------------------------------------------------------|
r_final: 0.2940
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.2863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  15989  Z= 0.202
  Angle     :  0.580  10.047  21752  Z= 0.303
  Chirality :  0.046   0.168   2602
  Planarity :  0.004   0.042   2740
  Dihedral  :  4.227  18.342   2292
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.62 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.19), residues: 2007
  helix:  2.14 (0.26), residues: 408
  sheet:  0.73 (0.22), residues: 550
  loop : -1.00 (0.18), residues: 1049

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP G 106 
 HIS   0.004   0.001   HIS F  34 
 PHE   0.023   0.001   PHE I  80 
 TYR   0.022   0.001   TYR D  49 
 ARG   0.007   0.001   ARG C 336 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 15628.27 seconds
wall clock time: 281 minutes 45.08 seconds (16905.08 seconds total)