Starting phenix.real_space_refine
on Fri Sep 19 04:29:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nri_12546/09_2025/7nri_12546.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nri_12546/09_2025/7nri_12546.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nri_12546/09_2025/7nri_12546.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nri_12546/09_2025/7nri_12546.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nri_12546/09_2025/7nri_12546.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nri_12546/09_2025/7nri_12546.cif"
  }
  resolution = 3.03
  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=   0.001 sd=   0.012
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: 5
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    7430      2.51       5
     N    2014      2.21       5
     O    2316      1.98       5
     H   11359      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 23151
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 12128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 785, 12128
          Classifications: {'peptide': 785}
          Link IDs: {'PTRANS': 29, 'TRANS': 755}
    Chain: "B"
      Number of atoms: 5416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 5416
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 11, 'TRANS': 350}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 844
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 6, 'TRANS': 51}
    Chain: "D"
      Number of atoms: 3346
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 3346
          Classifications: {'peptide': 209}
          Link IDs: {'PTRANS': 12, 'TRANS': 196}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1291
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1291
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 5, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 126
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 126
          Classifications: {'peptide': 7}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'UX8:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 4.34, per 1000 atoms: 0.19
  Number of scatterers: 23151
  At special positions: 0
  Unit cell: (99.22, 133.66, 125.46, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     O    2316      8.00
     N    2014      7.00
     C    7430      6.00
     H   11359      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 690 " - pdb=" SG  CYS A 700 " 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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.12
  Conformation dependent library (CDL) restraints added in 658.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2754

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 17 sheets defined
      22.3% alpha, 29.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 46
    Processing helix  chain 'A' and resid 55 through 69
    Processing helix  chain 'A' and resid 106 through 118
    Processing helix  chain 'A' and resid 129 through 145
    Processing helix  chain 'A' and resid 189 through 195
    Processing helix  chain 'A' and resid 215 through 232
    Processing helix  chain 'A' and resid 297 through 315
      removed outlier: 3.723A  pdb=" N   VAL A 301 " --> pdb=" O   ASN A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 367
      removed outlier: 3.739A  pdb=" N   LEU A 365 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 393
      removed outlier: 3.762A  pdb=" N   LEU A 392 " --> pdb=" O   ARG A 388 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   GLY A 393 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 500
      removed outlier: 3.955A  pdb=" N   ASP A 500 " --> pdb=" O   ASP A 497 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 497 through 500'
    Processing helix  chain 'A' and resid 542 through 552
      removed outlier: 4.372A  pdb=" N   TYR A 548 " --> pdb=" O   ALA A 544 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   SER A 551 " --> pdb=" O   ARG A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 691 through 695
      removed outlier: 3.584A  pdb=" N   GLY A 695 " --> pdb=" O   THR A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 729 through 733
      removed outlier: 3.643A  pdb=" N   VAL A 733 " --> pdb=" O   ALA A 730 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 31 through 35
    Processing helix  chain 'D' and resid 31 through 44
      removed outlier: 3.502A  pdb=" N   ILE D  35 " --> pdb=" O   PRO D  31 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   GLN D  44 " --> pdb=" O   GLN D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 61
      removed outlier: 4.365A  pdb=" N   ALA D  51 " --> pdb=" O   ASN D  47 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   THR D  53 " --> pdb=" O   ARG D  49 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLN D  54 " --> pdb=" O   GLN D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 82
    Processing helix  chain 'D' and resid 84 through 99
    Processing helix  chain 'D' and resid 102 through 104
      No H-bonds generated for 'chain 'D' and resid 102 through 104'
    Processing helix  chain 'D' and resid 105 through 121
    Processing helix  chain 'D' and resid 137 through 154
    Processing helix  chain 'D' and resid 160 through 189
      removed outlier: 3.825A  pdb=" N   PHE D 169 " --> pdb=" O   LYS D 165 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 191 through 205
      removed outlier: 3.865A  pdb=" N   VAL D 195 " --> pdb=" O   TRP D 191 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 213
      removed outlier: 3.883A  pdb=" N   ARG D 212 " --> pdb=" O   THR D 208 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 214 through 225
    Processing helix  chain 'D' and resid 227 through 240
      removed outlier: 3.531A  pdb=" N   ALA D 231 " --> pdb=" O   MET D 227 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   LYS D 233 " --> pdb=" O   ALA D 229 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 59
      removed outlier: 3.568A  pdb=" N   VAL E  55 " --> pdb=" O   THR E  51 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32
      removed outlier: 3.781A  pdb=" N   HIS A  30 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   VAL A  86 " --> pdb=" O   HIS A  30 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ASP A  74 " --> pdb=" O   LYS A  89 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100
      removed outlier: 7.532A  pdb=" N   LEU A 165 " --> pdb=" O   ALA A  95 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   ILE A  97 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   LEU A 167 " --> pdb=" O   ILE A  97 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   PHE A  99 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A  99 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183
      removed outlier: 7.667A  pdb=" N   VAL A 256 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   ILE A 180 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 7.539A  pdb=" N   VAL A 258 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   ILE A 182 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 7.267A  pdb=" N   ILE A 260 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER A 242 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   THR A 261 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 5.962A  pdb=" N   ILE A 240 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295
      removed outlier: 3.802A  pdb=" N   GLU A 294 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   LYS A 267 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 7.401A  pdb=" N   LEU A 337 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
      removed outlier: 8.427A  pdb=" N   SER A 269 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 12.742A  pdb=" N   VAL A 339 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
      removed outlier: 9.882A  pdb=" N   VAL A 271 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 12.327A  pdb=" N   VAL A 341 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 9.934A  pdb=" N   VAL A 273 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355
      removed outlier: 7.600A  pdb=" N   VAL A 414 " --> pdb=" O   ARG A 350 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   ILE A 352 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 7.177A  pdb=" N   TYR A 416 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   PHE A 354 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 7.397A  pdb=" N   VAL A 418 " --> pdb=" O   PHE A 354 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   GLN A 411 " --> pdb=" O   ARG A 404 " (cutoff:3.500A)
      removed outlier: 5.375A  pdb=" N   ARG A 404 " --> pdb=" O   GLN A 411 " (cutoff:3.500A)
      removed outlier: 5.761A  pdb=" N   ASP A 413 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   THR A 402 " --> pdb=" O   ASP A 413 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL A 415 " --> pdb=" O   THR A 400 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   THR A 400 " --> pdb=" O   VAL A 415 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   LYS A 417 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   VAL A 398 " --> pdb=" O   LYS A 417 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   LYS A 419 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 484 through 485
      removed outlier: 3.542A  pdb=" N   GLY A 516 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLN A 466 " --> pdb=" O   ASN A 463 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   PHE A 426 " --> pdb=" O   LYS G   5 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 484 through 485
      removed outlier: 3.542A  pdb=" N   GLY A 516 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   VAL A 784 " --> pdb=" O   ASN A 805 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   PHE A 426 " --> pdb=" O   LYS G   5 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 662 through 663
      removed outlier: 3.998A  pdb=" N   GLY A 662 " --> pdb=" O   GLU A 800 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 48 through 50
      removed outlier: 3.598A  pdb=" N   TRP B  48 " --> pdb=" O   SER B 389 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   LEU B 378 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 71 through 75
      removed outlier: 3.898A  pdb=" N   TRP B  93 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   ASN B  85 " --> pdb=" O   GLU B  91 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   GLU B  91 " --> pdb=" O   ASN B  85 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 116 through 117
    Processing sheet with id=AB3, first strand: chain 'B' and resid 156 through 158
      removed outlier: 3.664A  pdb=" N   TRP B 183 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 201 through 203
      removed outlier: 3.843A  pdb=" N   TRP B 228 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   LEU B 220 " --> pdb=" O   MET B 226 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   MET B 226 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 252 through 254
      removed outlier: 6.584A  pdb=" N   LEU B 267 " --> pdb=" O   LYS B 280 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   LYS B 280 " --> pdb=" O   LEU B 267 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   ALA B 269 " --> pdb=" O   MET B 278 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 290 through 292
      removed outlier: 6.983A  pdb=" N   VAL B 305 " --> pdb=" O   THR B 318 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   THR B 318 " --> pdb=" O   VAL B 305 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   ALA B 307 " --> pdb=" O   LEU B 316 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 331 through 333
    Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 35

    504 hydrogen bonds defined for protein.
    1389 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: 5.15

  Time building geometry restraints manager: 2.95 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 11321
        1.03 -     1.22: 39
        1.22 -     1.42: 5212
        1.42 -     1.61: 6775
        1.61 -     1.80: 63
  Bond restraints: 23410
  Sorted by residual:
  bond pdb=" C   TRP G   1 "
       pdb=" N   ASN G   2 "
    ideal  model  delta    sigma   weight residual
    1.329  1.452 -0.123 1.40e-02 5.10e+03 7.78e+01
  bond pdb=" CD2 PHE G   7 "
       pdb=" HD2 PHE G   7 "
    ideal  model  delta    sigma   weight residual
    0.930  1.090 -0.160 2.00e-02 2.50e+03 6.40e+01
  bond pdb=" CZ  PHE G   7 "
       pdb=" HZ  PHE G   7 "
    ideal  model  delta    sigma   weight residual
    0.930  1.089 -0.159 2.00e-02 2.50e+03 6.33e+01
  bond pdb=" CE3 UX8 G   3 "
       pdb=" HE3 UX8 G   3 "
    ideal  model  delta    sigma   weight residual
    0.930  1.089 -0.159 2.00e-02 2.50e+03 6.29e+01
  bond pdb=" CD1 PHE G   7 "
       pdb=" HD1 PHE G   7 "
    ideal  model  delta    sigma   weight residual
    0.930  1.088 -0.158 2.00e-02 2.50e+03 6.27e+01
  ... (remaining 23405 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.28: 42004
        3.28 -     6.56: 81
        6.56 -     9.84: 13
        9.84 -    13.12: 2
       13.12 -    16.40: 2
  Bond angle restraints: 42102
  Sorted by residual:
  angle pdb=" CA  TRP G   1 "
        pdb=" CB  TRP G   1 "
        pdb=" CG  TRP G   1 "
      ideal   model   delta    sigma   weight residual
     113.60   97.20   16.40 1.90e+00 2.77e-01 7.45e+01
  angle pdb=" CB  TRP G   1 "
        pdb=" CG  TRP G   1 "
        pdb=" CD2 TRP G   1 "
      ideal   model   delta    sigma   weight residual
     126.80  116.51   10.29 1.40e+00 5.10e-01 5.41e+01
  angle pdb=" CA  UX8 G   3 "
        pdb=" CB  UX8 G   3 "
        pdb=" O9  UX8 G   3 "
      ideal   model   delta    sigma   weight residual
     108.58   92.90   15.68 3.00e+00 1.11e-01 2.73e+01
  angle pdb=" CA  SER G   4 "
        pdb=" C   SER G   4 "
        pdb=" N   LYS G   5 "
      ideal   model   delta    sigma   weight residual
     116.20  126.31  -10.11 2.00e+00 2.50e-01 2.56e+01
  angle pdb=" C   TRP G   1 "
        pdb=" N   ASN G   2 "
        pdb=" CA  ASN G   2 "
      ideal   model   delta    sigma   weight residual
     121.70  130.18   -8.48 1.80e+00 3.09e-01 2.22e+01
  ... (remaining 42097 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 9927
       17.80 -    35.61: 870
       35.61 -    53.41: 244
       53.41 -    71.21: 46
       71.21 -    89.01: 9
  Dihedral angle restraints: 11096
    sinusoidal: 5974
      harmonic: 5122
  Sorted by residual:
  dihedral pdb=" C   UX8 G   3 "
           pdb=" N   UX8 G   3 "
           pdb=" CA  UX8 G   3 "
           pdb=" CB  UX8 G   3 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.22   15.62     0      2.50e+00 1.60e-01 3.90e+01
  dihedral pdb=" N   UX8 G   3 "
           pdb=" C   UX8 G   3 "
           pdb=" CA  UX8 G   3 "
           pdb=" CB  UX8 G   3 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  137.89  -15.09     0      2.50e+00 1.60e-01 3.64e+01
  dihedral pdb=" CA  LEU A 699 "
           pdb=" C   LEU A 699 "
           pdb=" N   CYS A 700 "
           pdb=" CA  CYS A 700 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.15  -25.85     0      5.00e+00 4.00e-02 2.67e+01
  ... (remaining 11093 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.154: 1777
       0.154 -    0.308: 1
       0.308 -    0.462: 0
       0.462 -    0.616: 1
       0.616 -    0.770: 1
  Chirality restraints: 1780
  Sorted by residual:
  chirality pdb=" CB  UX8 G   3 "
            pdb=" CA  UX8 G   3 "
            pdb=" CG  UX8 G   3 "
            pdb=" O9  UX8 G   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.38   -3.15    0.77 2.00e-01 2.50e+01 1.48e+01
  chirality pdb=" CA  UX8 G   3 "
            pdb=" N   UX8 G   3 "
            pdb=" C   UX8 G   3 "
            pdb=" CB  UX8 G   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.99    0.52 2.00e-01 2.50e+01 6.77e+00
  chirality pdb=" CA  TRP G   1 "
            pdb=" N   TRP G   1 "
            pdb=" C   TRP G   1 "
            pdb=" CB  TRP G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.57    2.33    0.23 2.00e-01 2.50e+01 1.35e+00
  ... (remaining 1777 not shown)

  Planarity restraints: 3590
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP G   1 "   -0.066 2.00e-02 2.50e+03   4.35e-02 7.10e+01
        pdb=" CG  TRP G   1 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP G   1 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP G   1 "    0.011 2.00e-02 2.50e+03
        pdb=" NE1 TRP G   1 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP G   1 "    0.109 2.00e-02 2.50e+03
        pdb=" CE3 TRP G   1 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ2 TRP G   1 "   -0.099 2.00e-02 2.50e+03
        pdb=" CZ3 TRP G   1 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP G   1 "    0.016 2.00e-02 2.50e+03
        pdb=" HD1 TRP G   1 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE1 TRP G   1 "   -0.011 2.00e-02 2.50e+03
        pdb=" HE3 TRP G   1 "    0.007 2.00e-02 2.50e+03
        pdb=" HZ3 TRP G   1 "    0.001 2.00e-02 2.50e+03
        pdb=" HH2 TRP G   1 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER G   4 "   -0.013 2.00e-02 2.50e+03   2.24e-02 5.03e+00
        pdb=" C   SER G   4 "    0.039 2.00e-02 2.50e+03
        pdb=" O   SER G   4 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LYS G   5 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  UX8 G   3 "   -0.022 2.00e-02 2.50e+03   1.12e-02 4.67e+00
        pdb=" CG  UX8 G   3 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD1 UX8 G   3 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 UX8 G   3 "    0.018 2.00e-02 2.50e+03
        pdb=" NE1 UX8 G   3 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 UX8 G   3 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 UX8 G   3 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ2 UX8 G   3 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ3 UX8 G   3 "    0.008 2.00e-02 2.50e+03
        pdb=" CH2 UX8 G   3 "   -0.003 2.00e-02 2.50e+03
        pdb=" HD1 UX8 G   3 "    0.009 2.00e-02 2.50e+03
        pdb=" HE1 UX8 G   3 "   -0.003 2.00e-02 2.50e+03
        pdb=" HE3 UX8 G   3 "    0.003 2.00e-02 2.50e+03
        pdb=" HZ2 UX8 G   3 "   -0.015 2.00e-02 2.50e+03
        pdb=" HZ3 UX8 G   3 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 3587 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.17: 944
        2.17 -     2.78: 44987
        2.78 -     3.39: 57870
        3.39 -     3.99: 79720
        3.99 -     4.60: 125231
  Nonbonded interactions: 308752
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 672 "
            pdb=" HG  SER A 702 "
     model   vdw
     1.566 2.450
  nonbonded pdb=" OD1 ASP B 384 "
            pdb=" HG1 THR B 386 "
     model   vdw
     1.570 2.450
  nonbonded pdb=" HE  ARG A 767 "
            pdb=" OD2 ASP A 797 "
     model   vdw
     1.598 2.450
  nonbonded pdb=" OD1 ASN B 350 "
            pdb=" H   VAL B 351 "
     model   vdw
     1.625 2.450
  nonbonded pdb=" HZ1 LYS A 146 "
            pdb=" OG  SER A 174 "
     model   vdw
     1.632 2.450
  ... (remaining 308747 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.470
  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:             0.150
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.040
  Process input model:                     21.660
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  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:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.129  12054  Z= 0.347
  Angle     :  0.636  16.395  16380  Z= 0.348
  Chirality :  0.049   0.770   1780
  Planarity :  0.004   0.053   2156
  Dihedral  : 14.467  89.014   4360
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.19 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  8.87 %
    Favored  : 90.81 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.46 (0.18), residues: 1486
  helix: -1.26 (0.26), residues: 314
  sheet: -1.84 (0.21), residues: 443
  loop : -3.09 (0.19), residues: 729

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  78 
 TYR   0.014   0.001   TYR A 509 
 PHE   0.014   0.001   PHE A 791 
 TRP   0.106   0.003   TRP G   1 
 HIS   0.004   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00719 (12051)
  covalent geometry    : angle       0.63473 (16378)
  SS BOND              : bond        0.00120 (    1)
  SS BOND              : angle       3.15382 (    2)
  hydrogen bonds       : bond        0.10775 (  500)
  hydrogen bonds       : angle       5.73259 ( 1389)
  Misc. bond           : bond        0.09104 (    2)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 160
  time to evaluate  : 0.559 
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: A  222 ASP cc_start: 0.7200 (m-30) cc_final: 0.6782 (m-30)
  outliers start: 4
  outliers final: 3
  residues processed: 164
  average time/residue: 0.3097
  time to fit residues: 67.5963
Evaluate side-chains
  102 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain E residue   42 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:    0.0470
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.6480

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

Flipped N/Q/H residues before XYZ refinement:
A 112 GLN
A 538 ASN
A 540 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.101646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.078487 restraints weight = 64762.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 2.36
r_work: 0.3161 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.1547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  12054  Z= 0.115
  Angle     :  0.500   7.981  16380  Z= 0.267
  Chirality :  0.043   0.140   1780
  Planarity :  0.003   0.035   2156
  Dihedral  :  4.356  27.390   1653
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 11.01 %
    Favored  : 88.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.42 (0.20), residues: 1486
  helix:  0.15 (0.28), residues: 322
  sheet: -1.46 (0.21), residues: 456
  loop : -2.56 (0.21), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  49 
 TYR   0.015   0.001   TYR D 184 
 PHE   0.010   0.001   PHE G   7 
 TRP   0.011   0.001   TRP B 348 
 HIS   0.003   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (12051)
  covalent geometry    : angle       0.49638 (16378)
  SS BOND              : bond        0.00177 (    1)
  SS BOND              : angle       5.75450 (    2)
  hydrogen bonds       : bond        0.03735 (  500)
  hydrogen bonds       : angle       4.80751 ( 1389)
  Misc. bond           : bond        0.00241 (    2)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.571 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ASP cc_start: 0.8215 (m-30) cc_final: 0.7638 (m-30)
REVERT: A  500 ASP cc_start: 0.7313 (t0) cc_final: 0.6789 (t0)
  outliers start: 7
  outliers final: 5
  residues processed: 109
  average time/residue: 0.2238
  time to fit residues: 35.4592
Evaluate side-chains
  99 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  614 ASP
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain D residue   52 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 146 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0970
   chunk 90 optimal weight:    2.9990
   chunk 1 optimal weight:   10.0000
   chunk 111 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 125 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
A 259 ASN
A 540 GLN
D  72 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.097353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.073747 restraints weight = 65548.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 2.37
r_work: 0.3092 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.2373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.094  12054  Z= 0.192
  Angle     :  0.519   6.200  16380  Z= 0.278
  Chirality :  0.043   0.141   1780
  Planarity :  0.004   0.041   2156
  Dihedral  :  4.344  21.074   1650
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 12.76 %
    Favored  : 86.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.78 (0.21), residues: 1486
  helix:  0.76 (0.29), residues: 324
  sheet: -1.15 (0.21), residues: 474
  loop : -2.16 (0.22), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 281 
 TYR   0.018   0.001   TYR A 757 
 PHE   0.011   0.001   PHE A 426 
 TRP   0.011   0.001   TRP A 546 
 HIS   0.004   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (12051)
  covalent geometry    : angle       0.51854 (16378)
  SS BOND              : bond        0.00496 (    1)
  SS BOND              : angle       2.81594 (    2)
  hydrogen bonds       : bond        0.03972 (  500)
  hydrogen bonds       : angle       4.63930 ( 1389)
  Misc. bond           : bond        0.00107 (    2)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ASP cc_start: 0.8280 (m-30) cc_final: 0.7735 (m-30)
REVERT: A  500 ASP cc_start: 0.7666 (t0) cc_final: 0.7157 (t0)
REVERT: A  701 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8587 (ttmt)
REVERT: B  226 MET cc_start: 0.8634 (ttt) cc_final: 0.8399 (mmm)
REVERT: B  283 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7398 (pp)
REVERT: D  134 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.7789 (m-30)
REVERT: E   84 GLU cc_start: 0.8099 (tp30) cc_final: 0.7833 (tp30)
REVERT: E  103 ASN cc_start: 0.8345 (t0) cc_final: 0.8143 (t0)
  outliers start: 15
  outliers final: 10
  residues processed: 106
  average time/residue: 0.2212
  time to fit residues: 34.5236
Evaluate side-chains
  97 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  355 GLU
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  601 ILE
Chi-restraints excluded: chain B residue  168 ASN
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain D residue   52 ILE
Chi-restraints excluded: chain D residue  134 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 89 optimal weight:    0.5980
   chunk 133 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 145 optimal weight:    1.9990
   chunk 134 optimal weight:    1.9990
   chunk 85 optimal weight:    0.6980
   chunk 115 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 7 optimal weight:    7.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
A 538 ASN
A 540 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.097107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.073357 restraints weight = 66099.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 2.38
r_work: 0.3061 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  12054  Z= 0.157
  Angle     :  0.486   7.605  16380  Z= 0.262
  Chirality :  0.043   0.138   1780
  Planarity :  0.003   0.043   2156
  Dihedral  :  4.285  24.324   1650
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 12.92 %
    Favored  : 86.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.39 (0.21), residues: 1486
  helix:  1.16 (0.29), residues: 318
  sheet: -0.84 (0.22), residues: 462
  loop : -1.98 (0.22), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  78 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.010   0.001   PHE A 791 
 TRP   0.010   0.001   TRP A 546 
 HIS   0.002   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (12051)
  covalent geometry    : angle       0.48433 (16378)
  SS BOND              : bond        0.00443 (    1)
  SS BOND              : angle       4.03621 (    2)
  hydrogen bonds       : bond        0.03629 (  500)
  hydrogen bonds       : angle       4.49390 ( 1389)
  Misc. bond           : bond        0.00078 (    2)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ASP cc_start: 0.8269 (m-30) cc_final: 0.7835 (m-30)
REVERT: A  500 ASP cc_start: 0.7674 (t0) cc_final: 0.7243 (t0)
REVERT: B  226 MET cc_start: 0.8652 (ttt) cc_final: 0.8401 (mmm)
REVERT: D  134 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.7800 (m-30)
  outliers start: 13
  outliers final: 8
  residues processed: 98
  average time/residue: 0.2558
  time to fit residues: 36.3614
Evaluate side-chains
  90 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  355 GLU
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  722 THR
Chi-restraints excluded: chain B residue  168 ASN
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain D residue  134 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 93 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 143 optimal weight:    1.9990
   chunk 141 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 5 optimal weight:    8.9990
   chunk 37 optimal weight:    2.9990
   chunk 138 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 540 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.097193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.073356 restraints weight = 65295.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 2.35
r_work: 0.3055 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.2945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  12054  Z= 0.154
  Angle     :  0.480   7.142  16380  Z= 0.257
  Chirality :  0.042   0.135   1780
  Planarity :  0.003   0.042   2156
  Dihedral  :  4.258  28.497   1650
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 2.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 13.15 %
    Favored  : 85.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.17 (0.21), residues: 1486
  helix:  1.47 (0.29), residues: 318
  sheet: -0.77 (0.22), residues: 469
  loop : -1.87 (0.22), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  78 
 TYR   0.015   0.001   TYR D 184 
 PHE   0.009   0.001   PHE A 791 
 TRP   0.012   0.001   TRP A 546 
 HIS   0.003   0.001   HIS D 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (12051)
  covalent geometry    : angle       0.47893 (16378)
  SS BOND              : bond        0.00939 (    1)
  SS BOND              : angle       2.85533 (    2)
  hydrogen bonds       : bond        0.03589 (  500)
  hydrogen bonds       : angle       4.42244 ( 1389)
  Misc. bond           : bond        0.00063 (    2)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ASP cc_start: 0.8296 (m-30) cc_final: 0.7855 (m-30)
REVERT: A  500 ASP cc_start: 0.7746 (t0) cc_final: 0.7401 (t0)
REVERT: A  540 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8309 (mm-40)
REVERT: B  226 MET cc_start: 0.8650 (ttt) cc_final: 0.8439 (mmm)
REVERT: D  134 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.7789 (m-30)
REVERT: E   47 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7253 (mtt-85)
  outliers start: 16
  outliers final: 12
  residues processed: 96
  average time/residue: 0.2270
  time to fit residues: 32.5441
Evaluate side-chains
  96 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  355 GLU
Chi-restraints excluded: chain A residue  540 GLN
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  700 CYS
Chi-restraints excluded: chain A residue  722 THR
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue  168 ASN
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain E residue   47 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   chunk 106 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 126 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 143 optimal weight:    1.9990
   chunk 122 optimal weight:    0.7980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 445 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.096726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.072932 restraints weight = 66154.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 2.38
r_work: 0.3052 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2936 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.3046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  12054  Z= 0.143
  Angle     :  0.471   5.773  16380  Z= 0.253
  Chirality :  0.042   0.135   1780
  Planarity :  0.003   0.043   2156
  Dihedral  :  4.221  25.948   1650
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 2.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 13.39 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.06 (0.21), residues: 1486
  helix:  1.57 (0.29), residues: 321
  sheet: -0.68 (0.22), residues: 469
  loop : -1.83 (0.22), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  78 
 TYR   0.015   0.001   TYR D 184 
 PHE   0.009   0.001   PHE A 791 
 TRP   0.013   0.001   TRP A 546 
 HIS   0.003   0.001   HIS D 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (12051)
  covalent geometry    : angle       0.47004 (16378)
  SS BOND              : bond        0.00409 (    1)
  SS BOND              : angle       3.33195 (    2)
  hydrogen bonds       : bond        0.03505 (  500)
  hydrogen bonds       : angle       4.37548 ( 1389)
  Misc. bond           : bond        0.00070 (    2)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ASP cc_start: 0.8314 (m-30) cc_final: 0.7874 (m-30)
REVERT: A  500 ASP cc_start: 0.7759 (t0) cc_final: 0.7413 (t0)
REVERT: B  226 MET cc_start: 0.8686 (ttt) cc_final: 0.8467 (mmm)
REVERT: D  134 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.7752 (m-30)
REVERT: D  205 TYR cc_start: 0.9340 (OUTLIER) cc_final: 0.8318 (m-80)
REVERT: E   47 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7326 (mtt-85)
  outliers start: 16
  outliers final: 13
  residues processed: 94
  average time/residue: 0.2436
  time to fit residues: 33.8448
Evaluate side-chains
  98 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  355 GLU
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  700 CYS
Chi-restraints excluded: chain A residue  722 THR
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue  168 ASN
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain E residue   47 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 82 optimal weight:    0.5980
   chunk 126 optimal weight:    0.0970
   chunk 44 optimal weight:    0.8980
   chunk 79 optimal weight:    0.6980
   chunk 139 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 3 optimal weight:    5.9990
   chunk 141 optimal weight:    0.5980
   chunk 97 optimal weight:    2.9990
   chunk 133 optimal weight:    1.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
A 540 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.098369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.074598 restraints weight = 65887.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 2.38
r_work: 0.3079 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.3182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  12054  Z= 0.091
  Angle     :  0.441   5.157  16380  Z= 0.235
  Chirality :  0.042   0.136   1780
  Planarity :  0.003   0.041   2156
  Dihedral  :  4.015  24.847   1650
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 13.47 %
    Favored  : 85.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.77 (0.21), residues: 1486
  helix:  1.89 (0.29), residues: 321
  sheet: -0.50 (0.22), residues: 470
  loop : -1.70 (0.22), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 120 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.005   0.001   PHE A 426 
 TRP   0.012   0.001   TRP A 546 
 HIS   0.004   0.001   HIS D 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 (12051)
  covalent geometry    : angle       0.44015 (16378)
  SS BOND              : bond        0.00428 (    1)
  SS BOND              : angle       2.14499 (    2)
  hydrogen bonds       : bond        0.03054 (  500)
  hydrogen bonds       : angle       4.19630 ( 1389)
  Misc. bond           : bond        0.00103 (    2)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ASP cc_start: 0.8279 (m-30) cc_final: 0.7817 (m-30)
REVERT: A  500 ASP cc_start: 0.7762 (t0) cc_final: 0.7358 (t0)
REVERT: D  205 TYR cc_start: 0.9342 (OUTLIER) cc_final: 0.8401 (m-80)
  outliers start: 13
  outliers final: 10
  residues processed: 95
  average time/residue: 0.2421
  time to fit residues: 33.9824
Evaluate side-chains
  92 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  540 GLN
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  700 CYS
Chi-restraints excluded: chain A residue  722 THR
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain D residue  205 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 109 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 143 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 5 optimal weight:   20.0000
   chunk 29 optimal weight:    0.9980
   chunk 146 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
B 266 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.095907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.072039 restraints weight = 66258.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 2.40
r_work: 0.3036 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.3276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076  12054  Z= 0.216
  Angle     :  0.487   5.862  16380  Z= 0.262
  Chirality :  0.043   0.136   1780
  Planarity :  0.004   0.052   2156
  Dihedral  :  4.179  23.151   1650
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 2.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 13.39 %
    Favored  : 85.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.21), residues: 1486
  helix:  1.78 (0.29), residues: 323
  sheet: -0.54 (0.22), residues: 474
  loop : -1.74 (0.22), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 120 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.012   0.001   PHE A 791 
 TRP   0.015   0.001   TRP A 546 
 HIS   0.007   0.001   HIS A 677 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 (12051)
  covalent geometry    : angle       0.48623 (16378)
  SS BOND              : bond        0.00286 (    1)
  SS BOND              : angle       3.09921 (    2)
  hydrogen bonds       : bond        0.03690 (  500)
  hydrogen bonds       : angle       4.33094 ( 1389)
  Misc. bond           : bond        0.00047 (    2)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ASP cc_start: 0.8333 (m-30) cc_final: 0.7783 (m-30)
REVERT: A  500 ASP cc_start: 0.7826 (t0) cc_final: 0.7297 (t0)
REVERT: D  134 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.7756 (m-30)
REVERT: D  205 TYR cc_start: 0.9349 (OUTLIER) cc_final: 0.8351 (m-80)
  outliers start: 17
  outliers final: 13
  residues processed: 93
  average time/residue: 0.2401
  time to fit residues: 32.9065
Evaluate side-chains
  94 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  355 GLU
Chi-restraints excluded: chain A residue  700 CYS
Chi-restraints excluded: chain A residue  722 THR
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue  168 ASN
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain D residue  205 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 144 optimal weight:    0.0970
   chunk 122 optimal weight:    3.9990
   chunk 138 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 141 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 132 optimal weight:    0.9980
   chunk 110 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   chunk 100 optimal weight:    0.6980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
A 445 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.097018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.073185 restraints weight = 66396.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 2.40
r_work: 0.3058 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.3357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  12054  Z= 0.099
  Angle     :  0.445   5.273  16380  Z= 0.238
  Chirality :  0.042   0.137   1780
  Planarity :  0.003   0.042   2156
  Dihedral  :  4.067  24.325   1650
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 1.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 13.47 %
    Favored  : 85.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.64 (0.21), residues: 1486
  helix:  1.99 (0.29), residues: 324
  sheet: -0.37 (0.23), residues: 470
  loop : -1.68 (0.22), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 120 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.006   0.001   PHE A 791 
 TRP   0.010   0.001   TRP B 348 
 HIS   0.004   0.001   HIS D 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (12051)
  covalent geometry    : angle       0.44415 (16378)
  SS BOND              : bond        0.00349 (    1)
  SS BOND              : angle       2.21013 (    2)
  hydrogen bonds       : bond        0.03187 (  500)
  hydrogen bonds       : angle       4.21141 ( 1389)
  Misc. bond           : bond        0.00103 (    2)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ASP cc_start: 0.8294 (m-30) cc_final: 0.7825 (m-30)
REVERT: A  500 ASP cc_start: 0.7788 (t0) cc_final: 0.7184 (t0)
REVERT: C   41 TYR cc_start: 0.7768 (p90) cc_final: 0.7543 (p90)
REVERT: D  134 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8045 (m-30)
REVERT: D  205 TYR cc_start: 0.9338 (OUTLIER) cc_final: 0.8431 (m-80)
  outliers start: 12
  outliers final: 9
  residues processed: 93
  average time/residue: 0.2393
  time to fit residues: 32.9249
Evaluate side-chains
  92 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  700 CYS
Chi-restraints excluded: chain A residue  722 THR
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain D residue  205 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 6 optimal weight:    8.9990
   chunk 142 optimal weight:    0.0060
   chunk 46 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 139 optimal weight:    0.6980
   chunk 103 optimal weight:    1.9990
   chunk 115 optimal weight:    0.6980
   chunk 12 optimal weight:    4.9990
   chunk 146 optimal weight:    0.9990
   overall best weight:    0.6800

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.098341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.074501 restraints weight = 66073.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 2.37
r_work: 0.3060 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.3437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  12054  Z= 0.103
  Angle     :  0.444   5.147  16380  Z= 0.237
  Chirality :  0.042   0.135   1780
  Planarity :  0.003   0.045   2156
  Dihedral  :  3.980  22.642   1650
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 1.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 13.63 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.48 (0.22), residues: 1486
  helix:  2.13 (0.29), residues: 324
  sheet: -0.27 (0.23), residues: 469
  loop : -1.58 (0.22), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 120 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.006   0.001   PHE A 791 
 TRP   0.014   0.001   TRP A 546 
 HIS   0.004   0.001   HIS D 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (12051)
  covalent geometry    : angle       0.44377 (16378)
  SS BOND              : bond        0.00276 (    1)
  SS BOND              : angle       2.21594 (    2)
  hydrogen bonds       : bond        0.03112 (  500)
  hydrogen bonds       : angle       4.14425 ( 1389)
  Misc. bond           : bond        0.00090 (    2)

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

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

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2972 Ramachandran restraints generated.
    1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 LYS cc_start: 0.9069 (mmtm) cc_final: 0.8861 (tptt)
REVERT: A  222 ASP cc_start: 0.8295 (m-30) cc_final: 0.7819 (m-30)
REVERT: A  500 ASP cc_start: 0.7788 (t0) cc_final: 0.7183 (t0)
REVERT: C   41 TYR cc_start: 0.7777 (p90) cc_final: 0.7514 (p90)
REVERT: D  134 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8078 (m-30)
REVERT: D  205 TYR cc_start: 0.9339 (OUTLIER) cc_final: 0.8521 (m-80)
  outliers start: 12
  outliers final: 9
  residues processed: 94
  average time/residue: 0.2366
  time to fit residues: 32.9416
Evaluate side-chains
  93 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  700 CYS
Chi-restraints excluded: chain A residue  722 THR
Chi-restraints excluded: chain A residue  736 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain D residue  205 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 143 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 131 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 64 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0060
   chunk 113 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.0002

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.096458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.072596 restraints weight = 66589.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 2.40
r_work: 0.3047 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.3516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12054  Z= 0.132
  Angle     :  0.456   5.189  16380  Z= 0.244
  Chirality :  0.042   0.135   1780
  Planarity :  0.003   0.043   2156
  Dihedral  :  4.033  22.289   1650
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 13.79 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.48 (0.22), residues: 1486
  helix:  2.11 (0.29), residues: 324
  sheet: -0.28 (0.23), residues: 471
  loop : -1.56 (0.23), residues: 691

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 120 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.009   0.001   PHE A 791 
 TRP   0.017   0.001   TRP A 546 
 HIS   0.004   0.001   HIS D 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (12051)
  covalent geometry    : angle       0.45487 (16378)
  SS BOND              : bond        0.00226 (    1)
  SS BOND              : angle       2.50759 (    2)
  hydrogen bonds       : bond        0.03311 (  500)
  hydrogen bonds       : angle       4.17575 ( 1389)
  Misc. bond           : bond        0.00070 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6060.03 seconds
wall clock time: 103 minutes 15.87 seconds (6195.87 seconds total)