Starting phenix.real_space_refine
on Sat Aug 23 13:08:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8odz_16820/08_2025/8odz_16820.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8odz_16820/08_2025/8odz_16820.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8odz_16820/08_2025/8odz_16820.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8odz_16820/08_2025/8odz_16820.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8odz_16820/08_2025/8odz_16820.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8odz_16820/08_2025/8odz_16820.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
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=   0.007
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      81      5.16       5
     C    7597      2.51       5
     N    2118      2.21       5
     O    2304      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12100
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1228
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 1228
          Classifications: {'peptide': 156}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 4, 'TRANS': 151}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 2336
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2336
          Classifications: {'peptide': 293}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "C"
      Number of atoms: 3854
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 485, 3854
          Classifications: {'peptide': 485}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 33, 'TRANS': 451}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "D"
      Number of atoms: 4561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 582, 4561
          Classifications: {'peptide': 582}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 541}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "E"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "C"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 3.14, per 1000 atoms: 0.26
  Number of scatterers: 12100
  At special positions: 0
  Unit cell: (87.58, 135.9, 194.79, 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      81     16.00
     O    2304      8.00
     N    2118      7.00
     C    7597      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=22, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  33 " - pdb=" SG  CYS A 106 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS A 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  81 " - pdb=" SG  CYS A 119 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  92 " - pdb=" SG  CYS B 197 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  50 " - pdb=" SG  CYS B  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 128 " - pdb=" SG  CYS B 139 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 167 " - pdb=" SG  CYS B 191 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 305 " - pdb=" SG  CYS B 331 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 311 " - pdb=" SG  CYS B 328 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  53 " - pdb=" SG  CYS C  63 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  81 " - pdb=" SG  CYS C  95 " distance=2.06
    Simple disulfide: pdb=" SG  CYS C 194 " - pdb=" SG  CYS C 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 252 " - pdb=" SG  CYS C 293 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 313 " - pdb=" SG  CYS C 390 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 315 " - pdb=" SG  CYS C 405 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 434 " - pdb=" SG  CYS C 495 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  28 " - pdb=" SG  CYS D 127 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  51 " - pdb=" SG  CYS D 111 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 145 " - pdb=" SG  CYS D 156 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 186 " - pdb=" SG  CYS D 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 432 " - pdb=" SG  CYS D 524 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 509 " - pdb=" SG  CYS D 567 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA E   3 " - " MAN E   4 "
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
    NAG-ASN
      " NAG C 601 " - " ASN C 169 "
      " NAG C 602 " - " ASN C 144 "
      " NAG C 603 " - " ASN C 463 "
      " NAG D 801 " - " ASN D 224 "
      " NAG D 802 " - " ASN D  48 "
      " NAG E   1 " - " ASN B 220 "
  Time building additional restraints: 0.99
  Conformation dependent library (CDL) restraints added in 595.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2870

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 33 sheets defined
      8.4% alpha, 36.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 55
      removed outlier: 3.698A  pdb=" N   GLN A  36 " --> pdb=" O   ARG A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 81
      removed outlier: 3.540A  pdb=" N   CYS A  81 " --> pdb=" O   THR A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 87
      removed outlier: 3.536A  pdb=" N   LEU A  86 " --> pdb=" O   PRO A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 112
      removed outlier: 3.724A  pdb=" N   THR A 112 " --> pdb=" O   PRO A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 141
      removed outlier: 3.778A  pdb=" N   CYS A 119 " --> pdb=" O   MET A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 167
      removed outlier: 4.555A  pdb=" N   LEU A 156 " --> pdb=" O   ASP A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 214
      removed outlier: 3.672A  pdb=" N   MET A 189 " --> pdb=" O   TYR A 185 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   THR A 200 " --> pdb=" O   HIS A 196 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 463 through 468
      removed outlier: 3.874A  pdb=" N   ALA C 467 " --> pdb=" O   ASN C 463 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 92
      No H-bonds generated for 'chain 'D' and resid 90 through 92'
    Processing helix  chain 'D' and resid 560 through 565
      removed outlier: 4.026A  pdb=" N   GLN D 564 " --> pdb=" O   PRO D 560 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   ARG D 565 " --> pdb=" O   PHE D 561 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 560 through 565'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 27
      removed outlier: 7.014A  pdb=" N   VAL B  30 " --> pdb=" O   LEU B  26 " (cutoff:3.500A)
      removed outlier: 5.183A  pdb=" N   THR B  96 " --> pdb=" O   LYS B  92 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   LYS B  92 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLY B  70 " --> pdb=" O   TRP B  60 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 35 through 36
    Processing sheet with id=AA3, first strand: chain 'B' and resid 44 through 49
    Processing sheet with id=AA4, first strand: chain 'B' and resid 117 through 118
      removed outlier: 4.245A  pdb=" N   LEU B 142 " --> pdb=" O   LYS B 118 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 117 through 118
      removed outlier: 4.245A  pdb=" N   LEU B 142 " --> pdb=" O   LYS B 118 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   GLU B 185 " --> pdb=" O   VAL B 143 " (cutoff:3.500A)
      removed outlier: 5.407A  pdb=" N   GLU B 175 " --> pdb=" O   LYS B 186 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   SER B 188 " --> pdb=" O   SER B 173 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   SER B 173 " --> pdb=" O   SER B 188 " (cutoff:3.500A)
      removed outlier: 7.318A  pdb=" N   SER B 190 " --> pdb=" O   SER B 171 " (cutoff:3.500A)
      removed outlier: 8.566A  pdb=" N   SER B 171 " --> pdb=" O   SER B 190 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 150
    Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 150
    Processing sheet with id=AA8, first strand: chain 'B' and resid 240 through 244
    Processing sheet with id=AA9, first strand: chain 'B' and resid 294 through 296
    Processing sheet with id=AB1, first strand: chain 'B' and resid 294 through 296
    Processing sheet with id=AB2, first strand: chain 'C' and resid 60 through 68
      removed outlier: 7.240A  pdb=" N   ASP C  60 " --> pdb=" O   ARG C  55 " (cutoff:3.500A)
      removed outlier: 5.005A  pdb=" N   ARG C  55 " --> pdb=" O   ASP C  60 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   GLU C  62 " --> pdb=" O   CYS C  53 " (cutoff:3.500A)
      removed outlier: 4.704A  pdb=" N   CYS C  53 " --> pdb=" O   GLU C  62 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   SER C  64 " --> pdb=" O   LEU C  51 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   LEU C  51 " --> pdb=" O   SER C  64 " (cutoff:3.500A)
      removed outlier: 8.121A  pdb=" N   LYS C 147 " --> pdb=" O   CYS C  53 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   ARG C  55 " --> pdb=" O   LYS C 147 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 94 through 99
    Processing sheet with id=AB4, first strand: chain 'C' and resid 94 through 99
      removed outlier: 3.651A  pdb=" N   VAL C 120 " --> pdb=" O   GLN C 140 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 156 through 160
    Processing sheet with id=AB6, first strand: chain 'C' and resid 189 through 193
    Processing sheet with id=AB7, first strand: chain 'C' and resid 276 through 279
    Processing sheet with id=AB8, first strand: chain 'C' and resid 320 through 324
    Processing sheet with id=AB9, first strand: chain 'C' and resid 368 through 372
      removed outlier: 3.561A  pdb=" N   GLY C 372 " --> pdb=" O   MET C 375 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   MET C 375 " --> pdb=" O   GLY C 372 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   MET C 378 " --> pdb=" O   HIS C 421 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   HIS C 421 " --> pdb=" O   MET C 378 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 404 through 408
      removed outlier: 4.495A  pdb=" N   HIS C 404 " --> pdb=" O   TRP C 393 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU C 455 " --> pdb=" O   VAL C 439 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   ALA C 441 " --> pdb=" O   THR C 453 " (cutoff:3.500A)
      removed outlier: 5.943A  pdb=" N   THR C 453 " --> pdb=" O   ALA C 441 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 471 through 477
      removed outlier: 6.294A  pdb=" N   HIS C 472 " --> pdb=" O   THR C 488 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   THR C 488 " --> pdb=" O   HIS C 472 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 514 through 519
      removed outlier: 3.535A  pdb=" N   VAL C 503 " --> pdb=" O   ARG C 542 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'D' and resid 31 through 36
    Processing sheet with id=AC5, first strand: chain 'D' and resid 40 through 41
      removed outlier: 3.654A  pdb=" N   CYS D 127 " --> pdb=" O   CYS D 111 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU D 108 " --> pdb=" O   PHE D  73 " (cutoff:3.500A)
      removed outlier: 8.083A  pdb=" N   LYS D  72 " --> pdb=" O   VAL D  79 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   VAL D  79 " --> pdb=" O   LYS D  72 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'D' and resid 196 through 198
      removed outlier: 4.297A  pdb=" N   ASN D 159 " --> pdb=" O   ASN D 142 " (cutoff:3.500A)
      removed outlier: 5.855A  pdb=" N   ASN D 142 " --> pdb=" O   ASN D 159 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   ILE D 239 " --> pdb=" O   CYS D 145 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   GLN D 147 " --> pdb=" O   ILE D 239 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'D' and resid 180 through 188
    Processing sheet with id=AC8, first strand: chain 'D' and resid 244 through 250
      removed outlier: 3.669A  pdb=" N   ILE D 246 " --> pdb=" O   GLN D 261 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   GLN D 261 " --> pdb=" O   ILE D 246 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   ILE D 248 " --> pdb=" O   THR D 259 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   THR D 259 " --> pdb=" O   ILE D 248 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'D' and resid 284 through 289
    Processing sheet with id=AD1, first strand: chain 'D' and resid 347 through 348
    Processing sheet with id=AD2, first strand: chain 'D' and resid 387 through 393
      removed outlier: 4.179A  pdb=" N   THR D 387 " --> pdb=" O   GLU D 382 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   TRP D 408 " --> pdb=" O   ILE D 428 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'D' and resid 443 through 448
      removed outlier: 4.419A  pdb=" N   GLU D 447 " --> pdb=" O   ASN D 451 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   ASN D 451 " --> pdb=" O   GLU D 447 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'D' and resid 487 through 491
      removed outlier: 4.117A  pdb=" N   GLU D 468 " --> pdb=" O   LEU D 517 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'D' and resid 544 through 548
    Processing sheet with id=AD6, first strand: chain 'D' and resid 585 through 590

    458 hydrogen bonds defined for protein.
    1185 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: 2.18

  Time building geometry restraints manager: 1.31 seconds

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

  Histogram of bond lengths:
        1.21 -     1.35: 3954
        1.35 -     1.49: 3128
        1.49 -     1.62: 5191
        1.62 -     1.76: 2
        1.76 -     1.90: 110
  Bond restraints: 12385
  Sorted by residual:
  bond pdb=" CB  PRO B  42 "
       pdb=" CG  PRO B  42 "
    ideal  model  delta    sigma   weight residual
    1.492  1.640 -0.148 5.00e-02 4.00e+02 8.73e+00
  bond pdb=" N   GLN B 248 "
       pdb=" CA  GLN B 248 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.16e-02 7.43e+03 8.66e+00
  bond pdb=" CB  CYS C  95 "
       pdb=" SG  CYS C  95 "
    ideal  model  delta    sigma   weight residual
    1.808  1.898 -0.090 3.30e-02 9.18e+02 7.48e+00
  bond pdb=" N   ASN A 145 "
       pdb=" CA  ASN A 145 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.032 1.18e-02 7.18e+03 7.14e+00
  bond pdb=" N   LYS B 245 "
       pdb=" CA  LYS B 245 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.036 1.34e-02 5.57e+03 7.07e+00
  ... (remaining 12380 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.02: 16753
        4.02 -     8.05: 71
        8.05 -    12.07: 10
       12.07 -    16.10: 0
       16.10 -    20.12: 1
  Bond angle restraints: 16835
  Sorted by residual:
  angle pdb=" CA  CYS C  81 "
        pdb=" CB  CYS C  81 "
        pdb=" SG  CYS C  81 "
      ideal   model   delta    sigma   weight residual
     114.40  134.52  -20.12 2.30e+00 1.89e-01 7.65e+01
  angle pdb=" CA  PRO B  42 "
        pdb=" N   PRO B  42 "
        pdb=" CD  PRO B  42 "
      ideal   model   delta    sigma   weight residual
     112.00  101.54   10.46 1.40e+00 5.10e-01 5.58e+01
  angle pdb=" N   CYS C  81 "
        pdb=" CA  CYS C  81 "
        pdb=" C   CYS C  81 "
      ideal   model   delta    sigma   weight residual
     108.60  116.88   -8.28 1.46e+00 4.69e-01 3.22e+01
  angle pdb=" CA  GLN B 248 "
        pdb=" C   GLN B 248 "
        pdb=" O   GLN B 248 "
      ideal   model   delta    sigma   weight residual
     121.89  115.87    6.02 1.27e+00 6.20e-01 2.25e+01
  angle pdb=" C   MET B 241 "
        pdb=" N   LYS B 242 "
        pdb=" CA  LYS B 242 "
      ideal   model   delta    sigma   weight residual
     120.94  129.67   -8.73 1.90e+00 2.77e-01 2.11e+01
  ... (remaining 16830 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.79: 6988
       20.79 -    41.57: 521
       41.57 -    62.36: 87
       62.36 -    83.14: 34
       83.14 -   103.93: 11
  Dihedral angle restraints: 7641
    sinusoidal: 3225
      harmonic: 4416
  Sorted by residual:
  dihedral pdb=" CB  CYS A  60 "
           pdb=" SG  CYS A  60 "
           pdb=" SG  CYS A 192 "
           pdb=" CB  CYS A 192 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.49  -80.49     1      1.00e+01 1.00e-02 8.01e+01
  dihedral pdb=" CB  CYS C 313 "
           pdb=" SG  CYS C 313 "
           pdb=" SG  CYS C 390 "
           pdb=" CB  CYS C 390 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -157.47   71.47     1      1.00e+01 1.00e-02 6.55e+01
  dihedral pdb=" CB  CYS C 194 "
           pdb=" SG  CYS C 194 "
           pdb=" SG  CYS C 216 "
           pdb=" CB  CYS C 216 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  152.22  -59.22     1      1.00e+01 1.00e-02 4.69e+01
  ... (remaining 7638 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.094: 1758
       0.094 -    0.187: 130
       0.187 -    0.281: 5
       0.281 -    0.375: 2
       0.375 -    0.469: 1
  Chirality restraints: 1896
  Sorted by residual:
  chirality pdb=" CB  ILE D 559 "
            pdb=" CA  ILE D 559 "
            pdb=" CG1 ILE D 559 "
            pdb=" CG2 ILE D 559 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.18    0.47 2.00e-01 2.50e+01 5.49e+00
  chirality pdb=" CA  CYS C  81 "
            pdb=" N   CYS C  81 "
            pdb=" C   CYS C  81 "
            pdb=" CB  CYS C  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.07e+00
  chirality pdb=" CA  PRO B  42 "
            pdb=" N   PRO B  42 "
            pdb=" C   PRO B  42 "
            pdb=" CB  PRO B  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.44    0.28 2.00e-01 2.50e+01 1.98e+00
  ... (remaining 1893 not shown)

  Planarity restraints: 2153
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 109 "    0.025 2.00e-02 2.50e+03   2.62e-02 1.71e+01
        pdb=" CG  TRP C 109 "   -0.070 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 109 "    0.036 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 109 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 109 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 109 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 109 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 109 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 109 "    0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 109 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 344 "    0.021 2.00e-02 2.50e+03   2.00e-02 1.00e+01
        pdb=" CG  TRP D 344 "   -0.054 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 344 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 344 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 344 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 344 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 344 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 344 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 344 "    0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 344 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B  41 "   -0.046 5.00e-02 4.00e+02   6.43e-02 6.62e+00
        pdb=" N   PRO B  42 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO B  42 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B  42 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 2150 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 901
        2.74 -     3.28: 11220
        3.28 -     3.82: 19404
        3.82 -     4.36: 21875
        4.36 -     4.90: 37808
  Nonbonded interactions: 91208
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D 233 "
            pdb=" OD1 ASP D 236 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OD2 ASP B 234 "
            pdb=" OG  SER B 258 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" ND2 ASN B 146 "
            pdb=" OE2 GLU B 185 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" O   PHE D  73 "
            pdb=" OG1 THR D 107 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OG  SER D 443 "
            pdb=" OG1 THR D 455 "
     model   vdw
     2.269 3.040
  ... (remaining 91203 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.750
  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:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     12.700
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  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:1.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
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   0.148  12416  Z= 0.192
  Angle     :  0.821  20.123  16906  Z= 0.426
  Chirality :  0.051   0.469   1896
  Planarity :  0.006   0.064   2147
  Dihedral  : 15.382 103.928   4705
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  0.52 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.87 (0.22), residues: 1488
  helix:  1.14 (0.53), residues: 98
  sheet:  0.18 (0.21), residues: 633
  loop : -1.50 (0.21), residues: 757

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 182 
 TYR   0.015   0.002   TYR A 124 
 PHE   0.019   0.002   PHE C 122 
 TRP   0.070   0.002   TRP C 109 
 HIS   0.004   0.001   HIS C 421 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 (12385)
  covalent geometry    : angle       0.80866 (16835)
  SS BOND              : bond        0.00615 (   22)
  SS BOND              : angle       2.00813 (   44)
  hydrogen bonds       : bond        0.11194 (  437)
  hydrogen bonds       : angle       6.60803 ( 1185)
  link_ALPHA1-3        : bond        0.00343 (    1)
  link_ALPHA1-3        : angle       1.87931 (    3)
  link_BETA1-4         : bond        0.00896 (    2)
  link_BETA1-4         : angle       1.86394 (    6)
  link_NAG-ASN         : bond        0.00352 (    6)
  link_NAG-ASN         : angle       3.01844 (   18)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  343 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 340
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 THR cc_start: 0.8666 (p) cc_final: 0.8035 (p)
REVERT: A   67 HIS cc_start: 0.8174 (t70) cc_final: 0.7790 (t70)
REVERT: A  141 LEU cc_start: 0.8713 (mt) cc_final: 0.8371 (mt)
REVERT: B  220 ASN cc_start: 0.6992 (m-40) cc_final: 0.6698 (m-40)
REVERT: B  246 ASN cc_start: 0.8494 (m-40) cc_final: 0.8243 (t0)
REVERT: C   50 ASN cc_start: 0.8264 (m-40) cc_final: 0.7799 (m-40)
REVERT: C   60 ASP cc_start: 0.8051 (t0) cc_final: 0.7757 (m-30)
REVERT: C   67 TYR cc_start: 0.7909 (t80) cc_final: 0.7583 (t80)
REVERT: C  167 ASP cc_start: 0.8449 (m-30) cc_final: 0.7725 (p0)
REVERT: C  329 LEU cc_start: 0.8503 (mt) cc_final: 0.8302 (mt)
REVERT: C  431 GLN cc_start: 0.8797 (mt0) cc_final: 0.8216 (mp10)
REVERT: D  158 TRP cc_start: 0.9018 (p90) cc_final: 0.8616 (p90)
REVERT: D  166 LEU cc_start: 0.9384 (tt) cc_final: 0.9092 (pp)
REVERT: D  189 ASP cc_start: 0.9319 (p0) cc_final: 0.9042 (p0)
REVERT: D  263 GLU cc_start: 0.8611 (tt0) cc_final: 0.8395 (tp30)
REVERT: D  295 TYR cc_start: 0.8928 (t80) cc_final: 0.8320 (t80)
REVERT: D  376 TYR cc_start: 0.8933 (m-80) cc_final: 0.8621 (m-80)
REVERT: D  449 MET cc_start: 0.8397 (ptt) cc_final: 0.8006 (ppp)
REVERT: D  540 PRO cc_start: 0.6748 (Cg_endo) cc_final: 0.6450 (Cg_exo)
REVERT: D  613 MET cc_start: 0.8280 (ppp) cc_final: 0.7979 (ppp)
  outliers start: 3
  outliers final: 0
  residues processed: 343
  average time/residue: 0.1224
  time to fit residues: 59.2924
Evaluate side-chains
  237 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    0.2980
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    0.0770
   chunk 91 optimal weight:    4.9990
   chunk 149 optimal weight:    8.9990
   overall best weight:    2.8744

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

Flipped N/Q/H residues before XYZ refinement:
A  87 HIS
A 145 ASN
B  87 GLN
B 101 HIS
C 163 GLN
** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 352 GLN
** C 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.157329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.102668 restraints weight = 29326.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.106731 restraints weight = 12383.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.109238 restraints weight = 7655.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.110734 restraints weight = 5794.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.111631 restraints weight = 4929.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.2449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.090  12416  Z= 0.324
  Angle     :  0.826  13.906  16906  Z= 0.419
  Chirality :  0.048   0.282   1896
  Planarity :  0.006   0.072   2147
  Dihedral  :  7.693  56.942   1813
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 16.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 14.16 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.22), residues: 1488
  helix:  1.05 (0.53), residues: 98
  sheet: -0.14 (0.21), residues: 616
  loop : -1.52 (0.21), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 565 
 TYR   0.028   0.002   TYR D 469 
 PHE   0.026   0.003   PHE C 180 
 TRP   0.045   0.003   TRP C 109 
 HIS   0.007   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00738 (12385)
  covalent geometry    : angle       0.80784 (16835)
  SS BOND              : bond        0.00710 (   22)
  SS BOND              : angle       1.95440 (   44)
  hydrogen bonds       : bond        0.05056 (  437)
  hydrogen bonds       : angle       5.99778 ( 1185)
  link_ALPHA1-3        : bond        0.00180 (    1)
  link_ALPHA1-3        : angle       2.67736 (    3)
  link_BETA1-4         : bond        0.00583 (    2)
  link_BETA1-4         : angle       1.91614 (    6)
  link_NAG-ASN         : bond        0.00867 (    6)
  link_NAG-ASN         : angle       4.38886 (   18)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 247
  time to evaluate  : 0.508 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 THR cc_start: 0.8846 (p) cc_final: 0.8406 (p)
REVERT: A   87 HIS cc_start: 0.4702 (OUTLIER) cc_final: 0.4202 (m-70)
REVERT: A  196 HIS cc_start: 0.7888 (t70) cc_final: 0.7291 (t-170)
REVERT: A  212 LEU cc_start: 0.9060 (tp) cc_final: 0.8828 (tp)
REVERT: B   60 TRP cc_start: 0.7945 (m100) cc_final: 0.7149 (m100)
REVERT: B  147 MET cc_start: 0.7711 (mtt) cc_final: 0.7292 (mtt)
REVERT: B  148 ASP cc_start: 0.7324 (t0) cc_final: 0.6989 (t0)
REVERT: B  269 LYS cc_start: 0.7638 (ttpt) cc_final: 0.7174 (ptpt)
REVERT: B  302 GLU cc_start: 0.7882 (tt0) cc_final: 0.7582 (tt0)
REVERT: C   50 ASN cc_start: 0.8446 (m-40) cc_final: 0.7948 (m-40)
REVERT: C   67 TYR cc_start: 0.8402 (t80) cc_final: 0.7852 (t80)
REVERT: C  167 ASP cc_start: 0.8474 (m-30) cc_final: 0.7683 (p0)
REVERT: C  226 GLU cc_start: 0.6360 (tp30) cc_final: 0.5880 (tp30)
REVERT: C  343 LYS cc_start: 0.6640 (OUTLIER) cc_final: 0.6198 (ttpt)
REVERT: C  431 GLN cc_start: 0.8971 (mt0) cc_final: 0.8365 (mp10)
REVERT: C  517 TRP cc_start: 0.8493 (m-90) cc_final: 0.8163 (m-90)
REVERT: D  189 ASP cc_start: 0.9140 (p0) cc_final: 0.8887 (p0)
REVERT: D  295 TYR cc_start: 0.8984 (t80) cc_final: 0.8486 (t80)
REVERT: D  449 MET cc_start: 0.8298 (ptt) cc_final: 0.7935 (ppp)
REVERT: D  540 PRO cc_start: 0.7535 (Cg_endo) cc_final: 0.6852 (Cg_exo)
REVERT: D  613 MET cc_start: 0.8523 (ppp) cc_final: 0.7971 (ppp)
  outliers start: 40
  outliers final: 28
  residues processed: 263
  average time/residue: 0.1055
  time to fit residues: 40.9901
Evaluate side-chains
  246 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 216
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue   70 ILE
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   87 HIS
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  138 ILE
Chi-restraints excluded: chain C residue  161 HIS
Chi-restraints excluded: chain C residue  256 GLU
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  301 VAL
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain C residue  524 THR
Chi-restraints excluded: chain C residue  559 SER
Chi-restraints excluded: chain D residue   34 THR
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  212 PHE
Chi-restraints excluded: chain D residue  233 THR
Chi-restraints excluded: chain D residue  290 ASN
Chi-restraints excluded: chain D residue  427 ASN
Chi-restraints excluded: chain D residue  432 CYS
Chi-restraints excluded: chain D residue  455 THR
Chi-restraints excluded: chain D residue  589 ILE
Chi-restraints excluded: chain D residue  611 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 149 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 143 optimal weight:    1.9990
   chunk 108 optimal weight:    4.9990
   chunk 85 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0050
   chunk 24 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.6794

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

Flipped N/Q/H residues before XYZ refinement:
A  87 HIS
B  87 GLN
B 246 ASN
** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 381 GLN
** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.160753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.106887 restraints weight = 29563.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.111280 restraints weight = 12085.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.114037 restraints weight = 7305.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.115631 restraints weight = 5430.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.116646 restraints weight = 4570.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.2598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  12416  Z= 0.137
  Angle     :  0.700  13.516  16906  Z= 0.348
  Chirality :  0.046   0.225   1896
  Planarity :  0.005   0.070   2147
  Dihedral  :  6.897  54.383   1813
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 16.68 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.83 (0.22), residues: 1488
  helix:  0.94 (0.51), residues: 103
  sheet:  0.19 (0.21), residues: 615
  loop : -1.41 (0.21), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 314 
 TYR   0.019   0.001   TYR D 275 
 PHE   0.026   0.002   PHE C 108 
 TRP   0.024   0.002   TRP D 398 
 HIS   0.005   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (12385)
  covalent geometry    : angle       0.68711 (16835)
  SS BOND              : bond        0.00406 (   22)
  SS BOND              : angle       1.45098 (   44)
  hydrogen bonds       : bond        0.04065 (  437)
  hydrogen bonds       : angle       5.58672 ( 1185)
  link_ALPHA1-3        : bond        0.00913 (    1)
  link_ALPHA1-3        : angle       2.17745 (    3)
  link_BETA1-4         : bond        0.00427 (    2)
  link_BETA1-4         : angle       1.64665 (    6)
  link_NAG-ASN         : bond        0.00246 (    6)
  link_NAG-ASN         : angle       3.41216 (   18)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 247
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 THR cc_start: 0.8847 (p) cc_final: 0.8449 (p)
REVERT: A   54 LYS cc_start: 0.8552 (mmtp) cc_final: 0.8339 (mmtp)
REVERT: A   58 TYR cc_start: 0.8007 (m-80) cc_final: 0.7708 (m-80)
REVERT: A  141 LEU cc_start: 0.8720 (mt) cc_final: 0.8423 (mt)
REVERT: A  196 HIS cc_start: 0.7767 (t70) cc_final: 0.7102 (t-170)
REVERT: A  212 LEU cc_start: 0.8970 (tp) cc_final: 0.8769 (tp)
REVERT: B   60 TRP cc_start: 0.7920 (m100) cc_final: 0.7250 (m100)
REVERT: B  133 TYR cc_start: 0.8550 (m-80) cc_final: 0.8303 (m-80)
REVERT: B  147 MET cc_start: 0.7569 (mtt) cc_final: 0.7177 (mtt)
REVERT: B  148 ASP cc_start: 0.7102 (t0) cc_final: 0.6707 (t0)
REVERT: B  246 ASN cc_start: 0.8130 (OUTLIER) cc_final: 0.7883 (t0)
REVERT: B  269 LYS cc_start: 0.7581 (ttpt) cc_final: 0.6856 (ptpp)
REVERT: B  302 GLU cc_start: 0.7811 (tt0) cc_final: 0.7473 (tt0)
REVERT: C   50 ASN cc_start: 0.8412 (m-40) cc_final: 0.7922 (m-40)
REVERT: C   60 ASP cc_start: 0.7891 (t0) cc_final: 0.7530 (m-30)
REVERT: C   67 TYR cc_start: 0.8308 (t80) cc_final: 0.7750 (t80)
REVERT: C  108 PHE cc_start: 0.8995 (p90) cc_final: 0.8783 (p90)
REVERT: C  167 ASP cc_start: 0.8429 (m-30) cc_final: 0.7624 (p0)
REVERT: C  214 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7166 (mt-10)
REVERT: C  329 LEU cc_start: 0.8461 (mt) cc_final: 0.8248 (mp)
REVERT: C  343 LYS cc_start: 0.6496 (OUTLIER) cc_final: 0.6064 (ttpt)
REVERT: C  431 GLN cc_start: 0.8876 (mt0) cc_final: 0.8246 (mp10)
REVERT: C  449 MET cc_start: 0.7872 (ppp) cc_final: 0.7650 (ppp)
REVERT: C  458 TYR cc_start: 0.7673 (m-10) cc_final: 0.7389 (m-10)
REVERT: C  548 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8759 (tp)
REVERT: D  166 LEU cc_start: 0.9190 (tt) cc_final: 0.8661 (pp)
REVERT: D  189 ASP cc_start: 0.9160 (p0) cc_final: 0.8856 (p0)
REVERT: D  295 TYR cc_start: 0.9002 (t80) cc_final: 0.8413 (t80)
REVERT: D  451 ASN cc_start: 0.9457 (t0) cc_final: 0.8811 (p0)
REVERT: D  540 PRO cc_start: 0.7532 (Cg_endo) cc_final: 0.6737 (Cg_exo)
REVERT: D  613 MET cc_start: 0.8410 (ppp) cc_final: 0.7896 (ppp)
  outliers start: 49
  outliers final: 24
  residues processed: 270
  average time/residue: 0.1071
  time to fit residues: 42.4107
Evaluate side-chains
  252 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 225
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue   70 ILE
Chi-restraints excluded: chain A residue   87 HIS
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  246 ASN
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  161 HIS
Chi-restraints excluded: chain C residue  249 MET
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  301 VAL
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain C residue  524 THR
Chi-restraints excluded: chain C residue  548 LEU
Chi-restraints excluded: chain C residue  559 SER
Chi-restraints excluded: chain D residue   34 THR
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  233 THR
Chi-restraints excluded: chain D residue  427 ASN
Chi-restraints excluded: chain D residue  432 CYS
Chi-restraints excluded: chain D residue  455 THR
Chi-restraints excluded: chain D residue  489 LEU
Chi-restraints excluded: chain D residue  589 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 148 optimal weight:    6.9990
   chunk 81 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 93 optimal weight:    0.0270
   chunk 31 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 129 optimal weight:    9.9990
   chunk 136 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 22 optimal weight:    7.9990
   chunk 85 optimal weight:    5.9990
   overall best weight:    0.9842

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

Flipped N/Q/H residues before XYZ refinement:
A  87 HIS
A 145 ASN
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 246 ASN
** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 190 ASN
D 252 ASN
** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.160468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.106401 restraints weight = 29322.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.110709 restraints weight = 12032.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.113368 restraints weight = 7302.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.114931 restraints weight = 5463.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.115855 restraints weight = 4616.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  12416  Z= 0.154
  Angle     :  0.678  12.733  16906  Z= 0.340
  Chirality :  0.045   0.254   1896
  Planarity :  0.005   0.068   2147
  Dihedral  :  6.452  54.467   1813
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 18.24 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.87 (0.22), residues: 1488
  helix:  0.88 (0.51), residues: 104
  sheet:  0.06 (0.21), residues: 620
  loop : -1.33 (0.21), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 233 
 TYR   0.013   0.001   TYR D 469 
 PHE   0.017   0.002   PHE C 108 
 TRP   0.024   0.002   TRP D 398 
 HIS   0.011   0.001   HIS D 570 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (12385)
  covalent geometry    : angle       0.66502 (16835)
  SS BOND              : bond        0.00409 (   22)
  SS BOND              : angle       1.47212 (   44)
  hydrogen bonds       : bond        0.03982 (  437)
  hydrogen bonds       : angle       5.49818 ( 1185)
  link_ALPHA1-3        : bond        0.00765 (    1)
  link_ALPHA1-3        : angle       2.13965 (    3)
  link_BETA1-4         : bond        0.00510 (    2)
  link_BETA1-4         : angle       1.61079 (    6)
  link_NAG-ASN         : bond        0.00171 (    6)
  link_NAG-ASN         : angle       3.26826 (   18)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 237
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 THR cc_start: 0.8857 (p) cc_final: 0.8534 (p)
REVERT: A   54 LYS cc_start: 0.8588 (mmtp) cc_final: 0.8321 (mmtp)
REVERT: A   58 TYR cc_start: 0.8017 (m-80) cc_final: 0.7649 (m-80)
REVERT: A  141 LEU cc_start: 0.8730 (mt) cc_final: 0.8424 (mt)
REVERT: A  196 HIS cc_start: 0.7772 (t70) cc_final: 0.7093 (t-170)
REVERT: A  212 LEU cc_start: 0.8974 (tp) cc_final: 0.8731 (tp)
REVERT: B   60 TRP cc_start: 0.7871 (m100) cc_final: 0.7166 (m100)
REVERT: B  133 TYR cc_start: 0.8577 (m-80) cc_final: 0.8281 (m-80)
REVERT: B  147 MET cc_start: 0.7572 (mtt) cc_final: 0.7169 (mtt)
REVERT: B  148 ASP cc_start: 0.7196 (t0) cc_final: 0.6786 (t0)
REVERT: B  269 LYS cc_start: 0.7497 (ttpt) cc_final: 0.6808 (ptpp)
REVERT: B  302 GLU cc_start: 0.7793 (tt0) cc_final: 0.7414 (tt0)
REVERT: C   50 ASN cc_start: 0.8413 (m-40) cc_final: 0.7948 (m-40)
REVERT: C   60 ASP cc_start: 0.7961 (t0) cc_final: 0.7580 (m-30)
REVERT: C   67 TYR cc_start: 0.8326 (t80) cc_final: 0.7819 (t80)
REVERT: C  108 PHE cc_start: 0.8932 (p90) cc_final: 0.8650 (p90)
REVERT: C  167 ASP cc_start: 0.8345 (m-30) cc_final: 0.7587 (p0)
REVERT: C  214 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7139 (mt-10)
REVERT: C  226 GLU cc_start: 0.6388 (tp30) cc_final: 0.6105 (tp30)
REVERT: C  314 ARG cc_start: 0.9181 (ttm-80) cc_final: 0.8970 (ttm-80)
REVERT: C  343 LYS cc_start: 0.6438 (OUTLIER) cc_final: 0.6019 (ttpt)
REVERT: C  431 GLN cc_start: 0.8851 (mt0) cc_final: 0.8222 (mp10)
REVERT: C  449 MET cc_start: 0.7859 (ppp) cc_final: 0.7610 (ppp)
REVERT: C  517 TRP cc_start: 0.8869 (m-90) cc_final: 0.8292 (m-90)
REVERT: C  548 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8735 (tp)
REVERT: D  147 GLN cc_start: 0.7543 (tt0) cc_final: 0.6846 (tp-100)
REVERT: D  166 LEU cc_start: 0.9194 (tt) cc_final: 0.8662 (pp)
REVERT: D  189 ASP cc_start: 0.9130 (p0) cc_final: 0.8803 (p0)
REVERT: D  260 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8831 (mt)
REVERT: D  295 TYR cc_start: 0.9064 (t80) cc_final: 0.8507 (t80)
REVERT: D  376 TYR cc_start: 0.9324 (OUTLIER) cc_final: 0.8983 (t80)
REVERT: D  451 ASN cc_start: 0.9417 (t0) cc_final: 0.8857 (p0)
REVERT: D  540 PRO cc_start: 0.7470 (Cg_endo) cc_final: 0.6722 (Cg_exo)
REVERT: D  613 MET cc_start: 0.8471 (ppp) cc_final: 0.8037 (ppp)
  outliers start: 42
  outliers final: 30
  residues processed: 251
  average time/residue: 0.1059
  time to fit residues: 39.2191
Evaluate side-chains
  261 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 227
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue   70 ILE
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   87 HIS
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  161 HIS
Chi-restraints excluded: chain C residue  249 MET
Chi-restraints excluded: chain C residue  256 GLU
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  301 VAL
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain C residue  548 LEU
Chi-restraints excluded: chain C residue  559 SER
Chi-restraints excluded: chain D residue   34 THR
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  260 LEU
Chi-restraints excluded: chain D residue  376 TYR
Chi-restraints excluded: chain D residue  427 ASN
Chi-restraints excluded: chain D residue  455 THR
Chi-restraints excluded: chain D residue  489 LEU
Chi-restraints excluded: chain D residue  589 ILE
Chi-restraints excluded: chain D residue  611 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 89 optimal weight:    8.9990
   chunk 5 optimal weight:    0.0270
   chunk 24 optimal weight:    0.5980
   chunk 114 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 142 optimal weight:    7.9990
   chunk 121 optimal weight:    8.9990
   chunk 93 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   overall best weight:    1.5244

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

Flipped N/Q/H residues before XYZ refinement:
A  87 HIS
** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.159034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.104471 restraints weight = 29489.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.108715 restraints weight = 12217.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.111315 restraints weight = 7429.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.112840 restraints weight = 5585.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.113775 restraints weight = 4745.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.3119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  12416  Z= 0.188
  Angle     :  0.689  11.426  16906  Z= 0.342
  Chirality :  0.044   0.226   1896
  Planarity :  0.005   0.065   2147
  Dihedral  :  6.224  54.249   1813
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 19.42 %
    Favored  : 76.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.84 (0.22), residues: 1488
  helix:  1.23 (0.52), residues: 98
  sheet:  0.10 (0.21), residues: 634
  loop : -1.39 (0.22), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 233 
 TYR   0.011   0.001   TYR D 574 
 PHE   0.028   0.002   PHE C 265 
 TRP   0.029   0.002   TRP D 398 
 HIS   0.005   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (12385)
  covalent geometry    : angle       0.67616 (16835)
  SS BOND              : bond        0.00391 (   22)
  SS BOND              : angle       1.35566 (   44)
  hydrogen bonds       : bond        0.04025 (  437)
  hydrogen bonds       : angle       5.45525 ( 1185)
  link_ALPHA1-3        : bond        0.00654 (    1)
  link_ALPHA1-3        : angle       2.34881 (    3)
  link_BETA1-4         : bond        0.00358 (    2)
  link_BETA1-4         : angle       1.53011 (    6)
  link_NAG-ASN         : bond        0.00468 (    6)
  link_NAG-ASN         : angle       3.54285 (   18)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 230
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 THR cc_start: 0.8904 (p) cc_final: 0.8501 (p)
REVERT: A  153 LYS cc_start: 0.8708 (ttpt) cc_final: 0.8131 (ttpp)
REVERT: A  185 TYR cc_start: 0.8651 (t80) cc_final: 0.8397 (t80)
REVERT: A  186 ARG cc_start: 0.7392 (mmt90) cc_final: 0.7167 (mmt90)
REVERT: A  196 HIS cc_start: 0.7835 (t70) cc_final: 0.7214 (t-170)
REVERT: B   60 TRP cc_start: 0.7855 (m100) cc_final: 0.7091 (m100)
REVERT: B  133 TYR cc_start: 0.8637 (m-80) cc_final: 0.8368 (m-80)
REVERT: B  147 MET cc_start: 0.7626 (mtt) cc_final: 0.7209 (mtt)
REVERT: B  148 ASP cc_start: 0.7369 (t0) cc_final: 0.6989 (t0)
REVERT: B  265 TYR cc_start: 0.7069 (t80) cc_final: 0.6834 (t80)
REVERT: C   50 ASN cc_start: 0.8438 (m-40) cc_final: 0.7973 (m-40)
REVERT: C   60 ASP cc_start: 0.8028 (t0) cc_final: 0.7612 (m-30)
REVERT: C   67 TYR cc_start: 0.8405 (t80) cc_final: 0.7825 (t80)
REVERT: C  167 ASP cc_start: 0.8315 (m-30) cc_final: 0.7613 (p0)
REVERT: C  214 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7156 (mt-10)
REVERT: C  226 GLU cc_start: 0.6343 (tp30) cc_final: 0.6025 (tp30)
REVERT: C  343 LYS cc_start: 0.6501 (OUTLIER) cc_final: 0.6069 (ttpt)
REVERT: C  431 GLN cc_start: 0.8870 (mt0) cc_final: 0.8243 (mp10)
REVERT: C  449 MET cc_start: 0.7896 (ppp) cc_final: 0.7632 (ppp)
REVERT: C  517 TRP cc_start: 0.8952 (m-90) cc_final: 0.8341 (m-90)
REVERT: C  548 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8468 (tp)
REVERT: D  147 GLN cc_start: 0.7753 (tt0) cc_final: 0.6898 (tp-100)
REVERT: D  166 LEU cc_start: 0.9222 (tt) cc_final: 0.8572 (pp)
REVERT: D  189 ASP cc_start: 0.9117 (p0) cc_final: 0.8799 (p0)
REVERT: D  260 LEU cc_start: 0.9207 (mt) cc_final: 0.8913 (mt)
REVERT: D  295 TYR cc_start: 0.9097 (t80) cc_final: 0.8537 (t80)
REVERT: D  376 TYR cc_start: 0.9401 (OUTLIER) cc_final: 0.8998 (t80)
REVERT: D  451 ASN cc_start: 0.9448 (t0) cc_final: 0.8828 (p0)
REVERT: D  540 PRO cc_start: 0.7447 (Cg_endo) cc_final: 0.6669 (Cg_exo)
REVERT: D  613 MET cc_start: 0.8503 (ppp) cc_final: 0.8059 (ppp)
  outliers start: 57
  outliers final: 39
  residues processed: 256
  average time/residue: 0.1033
  time to fit residues: 39.6402
Evaluate side-chains
  262 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 220
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue   70 ILE
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   87 HIS
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  161 HIS
Chi-restraints excluded: chain C residue  249 MET
Chi-restraints excluded: chain C residue  256 GLU
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  301 VAL
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain C residue  524 THR
Chi-restraints excluded: chain C residue  548 LEU
Chi-restraints excluded: chain D residue   34 THR
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  212 PHE
Chi-restraints excluded: chain D residue  233 THR
Chi-restraints excluded: chain D residue  248 ILE
Chi-restraints excluded: chain D residue  306 TYR
Chi-restraints excluded: chain D residue  376 TYR
Chi-restraints excluded: chain D residue  378 VAL
Chi-restraints excluded: chain D residue  427 ASN
Chi-restraints excluded: chain D residue  455 THR
Chi-restraints excluded: chain D residue  489 LEU
Chi-restraints excluded: chain D residue  589 ILE
Chi-restraints excluded: chain D residue  610 VAL
Chi-restraints excluded: chain D residue  611 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 105 optimal weight:    9.9990
   chunk 14 optimal weight:    0.6980
   chunk 95 optimal weight:    8.9990
   chunk 23 optimal weight:    1.9990
   chunk 130 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0170
   chunk 63 optimal weight:    0.0870
   chunk 106 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 136 optimal weight:    1.9990
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
A  87 HIS
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 GLN
B 214 GLN
B 246 ASN
** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.161032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.107430 restraints weight = 28997.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.111769 restraints weight = 12007.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.114399 restraints weight = 7264.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.115879 restraints weight = 5412.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.116893 restraints weight = 4581.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.091  12416  Z= 0.124
  Angle     :  0.667  13.535  16906  Z= 0.329
  Chirality :  0.044   0.227   1896
  Planarity :  0.005   0.063   2147
  Dihedral  :  5.956  54.862   1813
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 20.46 %
    Favored  : 75.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.67 (0.22), residues: 1488
  helix:  1.07 (0.51), residues: 104
  sheet:  0.28 (0.21), residues: 619
  loop : -1.29 (0.22), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 314 
 TYR   0.010   0.001   TYR D 574 
 PHE   0.041   0.002   PHE D 234 
 TRP   0.020   0.001   TRP D 344 
 HIS   0.003   0.001   HIS C 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (12385)
  covalent geometry    : angle       0.65468 (16835)
  SS BOND              : bond        0.00525 (   22)
  SS BOND              : angle       1.67306 (   44)
  hydrogen bonds       : bond        0.03671 (  437)
  hydrogen bonds       : angle       5.30573 ( 1185)
  link_ALPHA1-3        : bond        0.00860 (    1)
  link_ALPHA1-3        : angle       1.95574 (    3)
  link_BETA1-4         : bond        0.00550 (    2)
  link_BETA1-4         : angle       1.31582 (    6)
  link_NAG-ASN         : bond        0.00195 (    6)
  link_NAG-ASN         : angle       3.00507 (   18)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 234
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 THR cc_start: 0.8884 (p) cc_final: 0.8637 (p)
REVERT: A   54 LYS cc_start: 0.8867 (mmtp) cc_final: 0.8523 (mmtp)
REVERT: A  141 LEU cc_start: 0.8733 (mt) cc_final: 0.8431 (mt)
REVERT: A  153 LYS cc_start: 0.8641 (ttpt) cc_final: 0.8084 (ttpp)
REVERT: A  185 TYR cc_start: 0.8517 (t80) cc_final: 0.8043 (t80)
REVERT: B   60 TRP cc_start: 0.7776 (m100) cc_final: 0.7108 (m100)
REVERT: B  133 TYR cc_start: 0.8571 (m-80) cc_final: 0.8268 (m-80)
REVERT: B  147 MET cc_start: 0.7564 (mtt) cc_final: 0.7165 (mtt)
REVERT: B  148 ASP cc_start: 0.7203 (t0) cc_final: 0.6821 (t0)
REVERT: C   50 ASN cc_start: 0.8379 (m-40) cc_final: 0.7947 (m-40)
REVERT: C   60 ASP cc_start: 0.7946 (t0) cc_final: 0.7459 (m-30)
REVERT: C   67 TYR cc_start: 0.8303 (t80) cc_final: 0.7827 (t80)
REVERT: C  167 ASP cc_start: 0.8295 (m-30) cc_final: 0.7469 (p0)
REVERT: C  184 MET cc_start: 0.6576 (tpp) cc_final: 0.6287 (tpt)
REVERT: C  214 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7142 (mt-10)
REVERT: C  226 GLU cc_start: 0.6192 (tp30) cc_final: 0.5945 (tp30)
REVERT: C  343 LYS cc_start: 0.6427 (OUTLIER) cc_final: 0.5994 (ttpt)
REVERT: C  356 LEU cc_start: 0.8786 (mt) cc_final: 0.8483 (tt)
REVERT: C  431 GLN cc_start: 0.8768 (mt0) cc_final: 0.8135 (mp10)
REVERT: C  449 MET cc_start: 0.7899 (ppp) cc_final: 0.7638 (ppp)
REVERT: C  517 TRP cc_start: 0.8911 (m-90) cc_final: 0.8308 (m-90)
REVERT: C  548 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8403 (tp)
REVERT: D  147 GLN cc_start: 0.7743 (tt0) cc_final: 0.6885 (tp-100)
REVERT: D  166 LEU cc_start: 0.9251 (tt) cc_final: 0.8595 (pp)
REVERT: D  189 ASP cc_start: 0.9114 (p0) cc_final: 0.8748 (p0)
REVERT: D  260 LEU cc_start: 0.9175 (mt) cc_final: 0.8867 (mt)
REVERT: D  295 TYR cc_start: 0.9057 (t80) cc_final: 0.8475 (t80)
REVERT: D  376 TYR cc_start: 0.9399 (OUTLIER) cc_final: 0.8964 (t80)
REVERT: D  540 PRO cc_start: 0.7333 (Cg_endo) cc_final: 0.6565 (Cg_exo)
REVERT: D  613 MET cc_start: 0.8362 (ppp) cc_final: 0.7949 (ppp)
  outliers start: 55
  outliers final: 41
  residues processed: 261
  average time/residue: 0.1057
  time to fit residues: 40.7403
Evaluate side-chains
  269 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 225
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ILE
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   87 HIS
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  249 MET
Chi-restraints excluded: chain C residue  256 GLU
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  301 VAL
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain C residue  524 THR
Chi-restraints excluded: chain C residue  548 LEU
Chi-restraints excluded: chain C residue  559 SER
Chi-restraints excluded: chain D residue   34 THR
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  160 SER
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  212 PHE
Chi-restraints excluded: chain D residue  248 ILE
Chi-restraints excluded: chain D residue  306 TYR
Chi-restraints excluded: chain D residue  376 TYR
Chi-restraints excluded: chain D residue  378 VAL
Chi-restraints excluded: chain D residue  455 THR
Chi-restraints excluded: chain D residue  466 VAL
Chi-restraints excluded: chain D residue  489 LEU
Chi-restraints excluded: chain D residue  570 HIS
Chi-restraints excluded: chain D residue  589 ILE
Chi-restraints excluded: chain D residue  610 VAL
Chi-restraints excluded: chain D residue  611 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 106 optimal weight:    5.9990
   chunk 122 optimal weight:    9.9990
   chunk 91 optimal weight:    2.9990
   chunk 136 optimal weight:    3.9990
   chunk 149 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   chunk 139 optimal weight:    9.9990
   chunk 135 optimal weight:    6.9990
   chunk 56 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0010
   chunk 12 optimal weight:    2.9990
   overall best weight:    2.5994

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

Flipped N/Q/H residues before XYZ refinement:
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 246 ASN
C 111 GLN
** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 304 HIS
** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.156513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.101606 restraints weight = 29481.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.105713 restraints weight = 12375.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.108204 restraints weight = 7596.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.109665 restraints weight = 5735.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.110577 restraints weight = 4881.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.3597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.093  12416  Z= 0.287
  Angle     :  0.778  13.679  16906  Z= 0.385
  Chirality :  0.046   0.273   1896
  Planarity :  0.005   0.063   2147
  Dihedral  :  6.156  54.368   1813
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 17.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 20.98 %
    Favored  : 74.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.96 (0.22), residues: 1488
  helix:  1.03 (0.52), residues: 97
  sheet:  0.03 (0.21), residues: 642
  loop : -1.48 (0.22), residues: 749

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 233 
 TYR   0.015   0.002   TYR B 255 
 PHE   0.038   0.003   PHE C 108 
 TRP   0.024   0.002   TRP C 109 
 HIS   0.009   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00661 (12385)
  covalent geometry    : angle       0.76174 (16835)
  SS BOND              : bond        0.00655 (   22)
  SS BOND              : angle       1.37955 (   44)
  hydrogen bonds       : bond        0.04500 (  437)
  hydrogen bonds       : angle       5.65224 ( 1185)
  link_ALPHA1-3        : bond        0.00320 (    1)
  link_ALPHA1-3        : angle       2.46686 (    3)
  link_BETA1-4         : bond        0.00211 (    2)
  link_BETA1-4         : angle       1.74628 (    6)
  link_NAG-ASN         : bond        0.00793 (    6)
  link_NAG-ASN         : angle       4.30490 (   18)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 227
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.9374 (m-30) cc_final: 0.9044 (m-30)
REVERT: A   50 THR cc_start: 0.8946 (p) cc_final: 0.8676 (p)
REVERT: A  153 LYS cc_start: 0.8754 (ttpt) cc_final: 0.8202 (ttpp)
REVERT: A  196 HIS cc_start: 0.7915 (t70) cc_final: 0.7362 (t-170)
REVERT: B   60 TRP cc_start: 0.7865 (m100) cc_final: 0.6897 (m100)
REVERT: B   80 LYS cc_start: 0.8652 (pttp) cc_final: 0.7847 (mttt)
REVERT: B  133 TYR cc_start: 0.8659 (m-80) cc_final: 0.8407 (m-80)
REVERT: B  147 MET cc_start: 0.7722 (mtt) cc_final: 0.7365 (mtt)
REVERT: B  148 ASP cc_start: 0.7659 (t0) cc_final: 0.7323 (t0)
REVERT: B  201 GLU cc_start: 0.8002 (tp30) cc_final: 0.7202 (tp30)
REVERT: B  269 LYS cc_start: 0.7745 (pttt) cc_final: 0.6903 (ptpp)
REVERT: C   50 ASN cc_start: 0.8459 (m-40) cc_final: 0.7991 (m-40)
REVERT: C   60 ASP cc_start: 0.8095 (t0) cc_final: 0.7716 (m-30)
REVERT: C   67 TYR cc_start: 0.8508 (t80) cc_final: 0.7932 (t80)
REVERT: C  214 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7031 (mt-10)
REVERT: C  343 LYS cc_start: 0.6537 (OUTLIER) cc_final: 0.6089 (ttpt)
REVERT: C  431 GLN cc_start: 0.8888 (mt0) cc_final: 0.8245 (mp10)
REVERT: C  449 MET cc_start: 0.7945 (ppp) cc_final: 0.7709 (ppp)
REVERT: C  517 TRP cc_start: 0.9029 (m-90) cc_final: 0.8443 (m-90)
REVERT: C  548 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8495 (tp)
REVERT: D  147 GLN cc_start: 0.7930 (tt0) cc_final: 0.6995 (tp-100)
REVERT: D  189 ASP cc_start: 0.9095 (p0) cc_final: 0.8754 (p0)
REVERT: D  260 LEU cc_start: 0.9219 (mt) cc_final: 0.8951 (mt)
REVERT: D  295 TYR cc_start: 0.9160 (t80) cc_final: 0.8570 (t80)
REVERT: D  308 PHE cc_start: 0.9080 (m-80) cc_final: 0.8876 (m-80)
REVERT: D  376 TYR cc_start: 0.9497 (OUTLIER) cc_final: 0.9139 (t80)
REVERT: D  540 PRO cc_start: 0.7434 (Cg_endo) cc_final: 0.6676 (Cg_exo)
REVERT: D  613 MET cc_start: 0.8595 (ppp) cc_final: 0.8152 (ppp)
REVERT: D  621 GLU cc_start: 0.8933 (tt0) cc_final: 0.8250 (mp0)
  outliers start: 58
  outliers final: 48
  residues processed: 258
  average time/residue: 0.0942
  time to fit residues: 36.6866
Evaluate side-chains
  266 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 215
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue   70 ILE
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   87 HIS
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  123 ILE
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   91 HIS
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  206 ILE
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  249 MET
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  301 VAL
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain C residue  524 THR
Chi-restraints excluded: chain C residue  547 ARG
Chi-restraints excluded: chain C residue  548 LEU
Chi-restraints excluded: chain C residue  559 SER
Chi-restraints excluded: chain D residue   34 THR
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  160 SER
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  212 PHE
Chi-restraints excluded: chain D residue  233 THR
Chi-restraints excluded: chain D residue  248 ILE
Chi-restraints excluded: chain D residue  306 TYR
Chi-restraints excluded: chain D residue  376 TYR
Chi-restraints excluded: chain D residue  378 VAL
Chi-restraints excluded: chain D residue  455 THR
Chi-restraints excluded: chain D residue  466 VAL
Chi-restraints excluded: chain D residue  489 LEU
Chi-restraints excluded: chain D residue  589 ILE
Chi-restraints excluded: chain D residue  610 VAL
Chi-restraints excluded: chain D residue  611 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 131 optimal weight:    0.0870
   chunk 43 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A  87 HIS
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 246 ASN
** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 398 GLN
** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.160476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.105760 restraints weight = 28993.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.109886 restraints weight = 12311.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.112386 restraints weight = 7584.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.113904 restraints weight = 5724.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.114839 restraints weight = 4848.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.3565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.091  12416  Z= 0.126
  Angle     :  0.700  13.402  16906  Z= 0.340
  Chirality :  0.045   0.220   1896
  Planarity :  0.005   0.062   2147
  Dihedral  :  5.865  55.103   1813
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 21.79 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.69 (0.22), residues: 1488
  helix:  1.38 (0.52), residues: 98
  sheet:  0.29 (0.21), residues: 614
  loop : -1.35 (0.22), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 314 
 TYR   0.010   0.001   TYR D 574 
 PHE   0.027   0.001   PHE D 234 
 TRP   0.017   0.001   TRP C 123 
 HIS   0.003   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (12385)
  covalent geometry    : angle       0.68812 (16835)
  SS BOND              : bond        0.00372 (   22)
  SS BOND              : angle       1.55875 (   44)
  hydrogen bonds       : bond        0.03732 (  437)
  hydrogen bonds       : angle       5.31929 ( 1185)
  link_ALPHA1-3        : bond        0.00755 (    1)
  link_ALPHA1-3        : angle       1.76637 (    3)
  link_BETA1-4         : bond        0.00498 (    2)
  link_BETA1-4         : angle       1.21488 (    6)
  link_NAG-ASN         : bond        0.00221 (    6)
  link_NAG-ASN         : angle       3.17662 (   18)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 228
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.9281 (m-30) cc_final: 0.8864 (m-30)
REVERT: A   50 THR cc_start: 0.8951 (p) cc_final: 0.8750 (p)
REVERT: A   58 TYR cc_start: 0.7986 (m-80) cc_final: 0.7685 (m-80)
REVERT: A   74 GLN cc_start: 0.8708 (tp-100) cc_final: 0.8496 (tp-100)
REVERT: A  153 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8152 (ttpp)
REVERT: A  185 TYR cc_start: 0.8466 (t80) cc_final: 0.8232 (t80)
REVERT: B   60 TRP cc_start: 0.7785 (m100) cc_final: 0.7147 (m100)
REVERT: B   80 LYS cc_start: 0.8627 (pttp) cc_final: 0.7740 (mttt)
REVERT: B  133 TYR cc_start: 0.8590 (m-80) cc_final: 0.8344 (m-80)
REVERT: B  147 MET cc_start: 0.7587 (mtt) cc_final: 0.7144 (mtt)
REVERT: B  148 ASP cc_start: 0.7367 (t0) cc_final: 0.7027 (t0)
REVERT: B  211 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7708 (tp30)
REVERT: B  269 LYS cc_start: 0.7742 (pttt) cc_final: 0.6936 (ptpp)
REVERT: C   50 ASN cc_start: 0.8402 (m-40) cc_final: 0.7960 (m-40)
REVERT: C   60 ASP cc_start: 0.7963 (t0) cc_final: 0.7461 (m-30)
REVERT: C   67 TYR cc_start: 0.8361 (t80) cc_final: 0.7846 (t80)
REVERT: C  167 ASP cc_start: 0.8500 (m-30) cc_final: 0.7492 (p0)
REVERT: C  214 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7338 (mt-10)
REVERT: C  226 GLU cc_start: 0.6206 (tp30) cc_final: 0.5934 (tp30)
REVERT: C  343 LYS cc_start: 0.6459 (OUTLIER) cc_final: 0.6026 (ttpt)
REVERT: C  431 GLN cc_start: 0.8776 (mt0) cc_final: 0.8098 (mp10)
REVERT: C  449 MET cc_start: 0.7953 (ppp) cc_final: 0.7688 (ppp)
REVERT: C  517 TRP cc_start: 0.8988 (m-90) cc_final: 0.8403 (m-90)
REVERT: C  548 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8381 (tp)
REVERT: D   41 ILE cc_start: 0.9202 (tp) cc_final: 0.8897 (mm)
REVERT: D  147 GLN cc_start: 0.7837 (tt0) cc_final: 0.6912 (tp-100)
REVERT: D  166 LEU cc_start: 0.9275 (tt) cc_final: 0.8796 (pp)
REVERT: D  189 ASP cc_start: 0.9084 (p0) cc_final: 0.8703 (p0)
REVERT: D  260 LEU cc_start: 0.9223 (mt) cc_final: 0.8901 (mt)
REVERT: D  295 TYR cc_start: 0.9107 (t80) cc_final: 0.8527 (t80)
REVERT: D  376 TYR cc_start: 0.9478 (OUTLIER) cc_final: 0.9169 (t80)
REVERT: D  540 PRO cc_start: 0.7349 (Cg_endo) cc_final: 0.6633 (Cg_exo)
REVERT: D  613 MET cc_start: 0.8475 (ppp) cc_final: 0.8073 (ppp)
REVERT: D  621 GLU cc_start: 0.8884 (tt0) cc_final: 0.8194 (mp0)
  outliers start: 52
  outliers final: 38
  residues processed: 258
  average time/residue: 0.0989
  time to fit residues: 38.5323
Evaluate side-chains
  261 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 220
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 ILE
Chi-restraints excluded: chain A residue   87 HIS
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain B residue   38 THR
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  246 ASN
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  249 MET
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  301 VAL
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain C residue  405 CYS
Chi-restraints excluded: chain C residue  524 THR
Chi-restraints excluded: chain C residue  548 LEU
Chi-restraints excluded: chain C residue  559 SER
Chi-restraints excluded: chain D residue   34 THR
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  160 SER
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  248 ILE
Chi-restraints excluded: chain D residue  306 TYR
Chi-restraints excluded: chain D residue  314 LEU
Chi-restraints excluded: chain D residue  376 TYR
Chi-restraints excluded: chain D residue  378 VAL
Chi-restraints excluded: chain D residue  412 VAL
Chi-restraints excluded: chain D residue  455 THR
Chi-restraints excluded: chain D residue  466 VAL
Chi-restraints excluded: chain D residue  489 LEU
Chi-restraints excluded: chain D residue  589 ILE
Chi-restraints excluded: chain D residue  610 VAL
Chi-restraints excluded: chain D residue  611 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 146 optimal weight:    6.9990
   chunk 14 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 87 optimal weight:    4.9990
   chunk 137 optimal weight:    5.9990
   chunk 81 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 140 optimal weight:   20.0000
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A  87 HIS
A 145 ASN
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 246 ASN
** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 190 ASN
** D 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.159313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.104973 restraints weight = 29288.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.109166 restraints weight = 12244.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.111750 restraints weight = 7468.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 58)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.113285 restraints weight = 5582.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.114189 restraints weight = 4717.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.3676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12416  Z= 0.157
  Angle     :  0.717  12.713  16906  Z= 0.353
  Chirality :  0.045   0.236   1896
  Planarity :  0.005   0.061   2147
  Dihedral  :  5.791  54.741   1813
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 21.50 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.69 (0.22), residues: 1488
  helix:  1.41 (0.53), residues: 98
  sheet:  0.27 (0.21), residues: 617
  loop : -1.34 (0.22), residues: 773

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C 314 
 TYR   0.015   0.001   TYR D 469 
 PHE   0.023   0.002   PHE C 108 
 TRP   0.039   0.002   TRP D 398 
 HIS   0.007   0.001   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (12385)
  covalent geometry    : angle       0.69912 (16835)
  SS BOND              : bond        0.00526 (   22)
  SS BOND              : angle       2.28809 (   44)
  hydrogen bonds       : bond        0.03884 (  437)
  hydrogen bonds       : angle       5.36071 ( 1185)
  link_ALPHA1-3        : bond        0.00585 (    1)
  link_ALPHA1-3        : angle       1.81000 (    3)
  link_BETA1-4         : bond        0.00534 (    2)
  link_BETA1-4         : angle       1.28866 (    6)
  link_NAG-ASN         : bond        0.00320 (    6)
  link_NAG-ASN         : angle       3.34054 (   18)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 222
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 ASP cc_start: 0.9278 (m-30) cc_final: 0.8877 (m-30)
REVERT: A   58 TYR cc_start: 0.8016 (m-80) cc_final: 0.7713 (m-80)
REVERT: A   74 GLN cc_start: 0.8727 (tp-100) cc_final: 0.8474 (tp-100)
REVERT: A  153 LYS cc_start: 0.8690 (ttpt) cc_final: 0.8178 (ttpp)
REVERT: B   60 TRP cc_start: 0.7812 (m100) cc_final: 0.7056 (m100)
REVERT: B   80 LYS cc_start: 0.8640 (pttp) cc_final: 0.7757 (mttt)
REVERT: B  133 TYR cc_start: 0.8648 (m-80) cc_final: 0.8388 (m-80)
REVERT: B  147 MET cc_start: 0.7612 (mtt) cc_final: 0.7275 (mtt)
REVERT: B  148 ASP cc_start: 0.7420 (t0) cc_final: 0.7105 (t0)
REVERT: B  269 LYS cc_start: 0.7770 (pttt) cc_final: 0.6988 (ptpp)
REVERT: C   50 ASN cc_start: 0.8402 (m-40) cc_final: 0.7964 (m-40)
REVERT: C   60 ASP cc_start: 0.7976 (t0) cc_final: 0.7554 (m-30)
REVERT: C   67 TYR cc_start: 0.8386 (t80) cc_final: 0.7815 (t80)
REVERT: C  167 ASP cc_start: 0.8460 (m-30) cc_final: 0.7493 (p0)
REVERT: C  214 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7150 (mt-10)
REVERT: C  226 GLU cc_start: 0.6227 (tp30) cc_final: 0.6013 (tp30)
REVERT: C  280 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8009 (tpp)
REVERT: C  343 LYS cc_start: 0.6537 (OUTLIER) cc_final: 0.6086 (ttpt)
REVERT: C  431 GLN cc_start: 0.8786 (mt0) cc_final: 0.8111 (mp10)
REVERT: C  449 MET cc_start: 0.7961 (ppp) cc_final: 0.7712 (ppp)
REVERT: C  517 TRP cc_start: 0.9011 (m-90) cc_final: 0.8303 (m-90)
REVERT: C  518 LEU cc_start: 0.9231 (mm) cc_final: 0.8951 (mm)
REVERT: C  548 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8370 (tp)
REVERT: D  147 GLN cc_start: 0.7875 (tt0) cc_final: 0.6968 (tp-100)
REVERT: D  189 ASP cc_start: 0.9060 (p0) cc_final: 0.8690 (p0)
REVERT: D  260 LEU cc_start: 0.9202 (mt) cc_final: 0.8890 (mt)
REVERT: D  295 TYR cc_start: 0.9110 (t80) cc_final: 0.8546 (t80)
REVERT: D  376 TYR cc_start: 0.9475 (OUTLIER) cc_final: 0.9187 (t80)
REVERT: D  540 PRO cc_start: 0.7235 (Cg_endo) cc_final: 0.6510 (Cg_exo)
REVERT: D  551 ARG cc_start: 0.8931 (mmp-170) cc_final: 0.8716 (mmp-170)
REVERT: D  613 MET cc_start: 0.8444 (ppp) cc_final: 0.8027 (ppp)
REVERT: D  621 GLU cc_start: 0.8875 (tt0) cc_final: 0.8188 (mp0)
  outliers start: 56
  outliers final: 44
  residues processed: 251
  average time/residue: 0.0761
  time to fit residues: 28.5941
Evaluate side-chains
  261 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 213
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue   70 ILE
Chi-restraints excluded: chain A residue   87 HIS
Chi-restraints excluded: chain A residue  146 HIS
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   38 THR
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  246 ASN
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  249 MET
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  280 MET
Chi-restraints excluded: chain C residue  301 VAL
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain C residue  405 CYS
Chi-restraints excluded: chain C residue  524 THR
Chi-restraints excluded: chain C residue  548 LEU
Chi-restraints excluded: chain C residue  559 SER
Chi-restraints excluded: chain D residue   34 THR
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue  127 CYS
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  160 SER
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  212 PHE
Chi-restraints excluded: chain D residue  248 ILE
Chi-restraints excluded: chain D residue  306 TYR
Chi-restraints excluded: chain D residue  314 LEU
Chi-restraints excluded: chain D residue  376 TYR
Chi-restraints excluded: chain D residue  378 VAL
Chi-restraints excluded: chain D residue  412 VAL
Chi-restraints excluded: chain D residue  432 CYS
Chi-restraints excluded: chain D residue  455 THR
Chi-restraints excluded: chain D residue  466 VAL
Chi-restraints excluded: chain D residue  489 LEU
Chi-restraints excluded: chain D residue  589 ILE
Chi-restraints excluded: chain D residue  610 VAL
Chi-restraints excluded: chain D residue  611 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 139 optimal weight:    0.9990
   chunk 132 optimal weight:    9.9990
   chunk 144 optimal weight:    6.9990
   chunk 74 optimal weight:   10.0000
   chunk 122 optimal weight:    3.9990
   chunk 54 optimal weight:   10.0000
   chunk 47 optimal weight:    0.8980
   chunk 92 optimal weight:    6.9990
   chunk 110 optimal weight:    1.9990
   chunk 136 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A  87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 GLN
B 246 ASN
** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.158025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.102974 restraints weight = 29161.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.106921 restraints weight = 12515.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.109344 restraints weight = 7771.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.110773 restraints weight = 5895.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.111665 restraints weight = 5022.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.3861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.079  12416  Z= 0.216
  Angle     :  0.759  12.810  16906  Z= 0.376
  Chirality :  0.046   0.267   1896
  Planarity :  0.005   0.070   2147
  Dihedral  :  5.920  54.565   1813
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 16.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 22.54 %
    Favored  : 73.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.81 (0.22), residues: 1488
  helix:  1.34 (0.53), residues: 98
  sheet:  0.14 (0.21), residues: 634
  loop : -1.40 (0.22), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 314 
 TYR   0.013   0.002   TYR B 265 
 PHE   0.026   0.002   PHE C 108 
 TRP   0.030   0.002   TRP C 393 
 HIS   0.007   0.001   HIS C 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 (12385)
  covalent geometry    : angle       0.74225 (16835)
  SS BOND              : bond        0.00682 (   22)
  SS BOND              : angle       2.03220 (   44)
  hydrogen bonds       : bond        0.04136 (  437)
  hydrogen bonds       : angle       5.51293 ( 1185)
  link_ALPHA1-3        : bond        0.00335 (    1)
  link_ALPHA1-3        : angle       1.98574 (    3)
  link_BETA1-4         : bond        0.00310 (    2)
  link_BETA1-4         : angle       1.46394 (    6)
  link_NAG-ASN         : bond        0.00536 (    6)
  link_NAG-ASN         : angle       3.70508 (   18)

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

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

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2976 Ramachandran restraints generated.
    1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 214
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLN cc_start: 0.8779 (tp-100) cc_final: 0.8521 (tp-100)
REVERT: A  153 LYS cc_start: 0.8730 (ttpt) cc_final: 0.8201 (ttpp)
REVERT: B   60 TRP cc_start: 0.7856 (m100) cc_final: 0.7074 (m100)
REVERT: B   80 LYS cc_start: 0.8643 (pttp) cc_final: 0.7792 (mttt)
REVERT: B  133 TYR cc_start: 0.8643 (m-80) cc_final: 0.8367 (m-80)
REVERT: B  147 MET cc_start: 0.7646 (mtt) cc_final: 0.7209 (mtt)
REVERT: B  148 ASP cc_start: 0.7563 (t0) cc_final: 0.7249 (t0)
REVERT: B  269 LYS cc_start: 0.7791 (pttt) cc_final: 0.7034 (ptpp)
REVERT: C   50 ASN cc_start: 0.8436 (m-40) cc_final: 0.7983 (m-40)
REVERT: C   60 ASP cc_start: 0.8040 (t0) cc_final: 0.7583 (m-30)
REVERT: C   67 TYR cc_start: 0.8455 (t80) cc_final: 0.7909 (t80)
REVERT: C  167 ASP cc_start: 0.8447 (m-30) cc_final: 0.7439 (p0)
REVERT: C  214 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7088 (mt-10)
REVERT: C  226 GLU cc_start: 0.6312 (tp30) cc_final: 0.6045 (tp30)
REVERT: C  280 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8033 (tpp)
REVERT: C  343 LYS cc_start: 0.6553 (OUTLIER) cc_final: 0.6092 (ttpt)
REVERT: C  431 GLN cc_start: 0.8825 (mt0) cc_final: 0.8158 (mp10)
REVERT: C  449 MET cc_start: 0.7929 (ppp) cc_final: 0.7679 (ppp)
REVERT: C  517 TRP cc_start: 0.9026 (m-90) cc_final: 0.8444 (m-90)
REVERT: C  548 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8391 (tp)
REVERT: D  147 GLN cc_start: 0.7944 (tt0) cc_final: 0.7001 (tp-100)
REVERT: D  189 ASP cc_start: 0.9054 (p0) cc_final: 0.8749 (p0)
REVERT: D  260 LEU cc_start: 0.9241 (mt) cc_final: 0.8947 (mt)
REVERT: D  295 TYR cc_start: 0.9148 (t80) cc_final: 0.8562 (t80)
REVERT: D  376 TYR cc_start: 0.9491 (OUTLIER) cc_final: 0.9202 (t80)
REVERT: D  540 PRO cc_start: 0.7329 (Cg_endo) cc_final: 0.6612 (Cg_exo)
REVERT: D  613 MET cc_start: 0.8515 (ppp) cc_final: 0.8093 (ppp)
REVERT: D  621 GLU cc_start: 0.8931 (tt0) cc_final: 0.8263 (mp0)
  outliers start: 49
  outliers final: 42
  residues processed: 241
  average time/residue: 0.0808
  time to fit residues: 29.7185
Evaluate side-chains
  257 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 211
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue   70 ILE
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   38 THR
Chi-restraints excluded: chain B residue   46 VAL
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain C residue  249 MET
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  278 LEU
Chi-restraints excluded: chain C residue  280 MET
Chi-restraints excluded: chain C residue  301 VAL
Chi-restraints excluded: chain C residue  343 LYS
Chi-restraints excluded: chain C residue  524 THR
Chi-restraints excluded: chain C residue  548 LEU
Chi-restraints excluded: chain C residue  559 SER
Chi-restraints excluded: chain D residue   34 THR
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  127 CYS
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  160 SER
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  212 PHE
Chi-restraints excluded: chain D residue  248 ILE
Chi-restraints excluded: chain D residue  306 TYR
Chi-restraints excluded: chain D residue  314 LEU
Chi-restraints excluded: chain D residue  376 TYR
Chi-restraints excluded: chain D residue  378 VAL
Chi-restraints excluded: chain D residue  412 VAL
Chi-restraints excluded: chain D residue  432 CYS
Chi-restraints excluded: chain D residue  455 THR
Chi-restraints excluded: chain D residue  466 VAL
Chi-restraints excluded: chain D residue  489 LEU
Chi-restraints excluded: chain D residue  570 HIS
Chi-restraints excluded: chain D residue  589 ILE
Chi-restraints excluded: chain D residue  610 VAL
Chi-restraints excluded: chain D residue  611 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 41 optimal weight:    6.9990
   chunk 81 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 139 optimal weight:    2.9990
   chunk 113 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 137 optimal weight:    5.9990
   chunk 118 optimal weight:    0.9990
   chunk 96 optimal weight:    8.9990
   chunk 112 optimal weight:   10.0000
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A  87 HIS
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 246 ASN
** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.157593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.102920 restraints weight = 29170.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.106821 restraints weight = 12479.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.109223 restraints weight = 7744.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.110664 restraints weight = 5876.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.111485 restraints weight = 4996.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.3996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077  12416  Z= 0.211
  Angle     :  0.748  12.657  16906  Z= 0.370
  Chirality :  0.046   0.286   1896
  Planarity :  0.005   0.069   2147
  Dihedral  :  5.958  54.693   1813
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 16.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 22.54 %
    Favored  : 73.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.88 (0.22), residues: 1488
  helix:  1.10 (0.52), residues: 99
  sheet:  0.10 (0.21), residues: 634
  loop : -1.44 (0.22), residues: 755

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 314 
 TYR   0.014   0.002   TYR B 265 
 PHE   0.024   0.002   PHE C 108 
 TRP   0.053   0.002   TRP D 398 
 HIS   0.007   0.001   HIS C 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 (12385)
  covalent geometry    : angle       0.73275 (16835)
  SS BOND              : bond        0.00476 (   22)
  SS BOND              : angle       1.81113 (   44)
  hydrogen bonds       : bond        0.04220 (  437)
  hydrogen bonds       : angle       5.57913 ( 1185)
  link_ALPHA1-3        : bond        0.00343 (    1)
  link_ALPHA1-3        : angle       2.01782 (    3)
  link_BETA1-4         : bond        0.00362 (    2)
  link_BETA1-4         : angle       1.42426 (    6)
  link_NAG-ASN         : bond        0.00531 (    6)
  link_NAG-ASN         : angle       3.80881 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3435.91 seconds
wall clock time: 59 minutes 43.98 seconds (3583.98 seconds total)