Starting phenix.real_space_refine
on Thu Mar  5 08:22:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tt4_26110/03_2026/7tt4_26110.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tt4_26110/03_2026/7tt4_26110.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tt4_26110/03_2026/7tt4_26110.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tt4_26110/03_2026/7tt4_26110.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tt4_26110/03_2026/7tt4_26110.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tt4_26110/03_2026/7tt4_26110.map"
  }
  resolution = 4.2
  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=   0.006 sd=   0.065
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    6637      2.51       5
     N    1794      2.21       5
     O    2063      1.98       5
     H   10107      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 62 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 20633
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 9595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 621, 9595
          Classifications: {'peptide': 621}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 24, 'TRANS': 596}
          Chain breaks: 3
    Chain: "P"
      Number of atoms: 393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 393
          Classifications: {'peptide': 25}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 24}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 3390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 3390
          Classifications: {'peptide': 213}
          Link IDs: {'PTRANS': 10, 'TRANS': 202}
    Chain: "C"
      Number of atoms: 675
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 675
          Classifications: {'peptide': 48}
          Link IDs: {'PTRANS': 6, 'TRANS': 41}
    Chain: "E"
      Number of atoms: 1381
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 1381
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 5, 'TRANS': 83}
    Chain: "B"
      Number of atoms: 5199
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 350, 5199
          Classifications: {'peptide': 350}
          Link IDs: {'PTRANS': 11, 'TRANS': 338}
          Chain breaks: 2
  Time building chain proxies: 3.68, per 1000 atoms: 0.18
  Number of scatterers: 20633
  At special positions: 0
  Unit cell: (108.456, 124.563, 138.523, 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    2063      8.00
     N    1794      7.00
     C    6637      6.00
     H   10107      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 425 " - pdb=" SG  CYS P1299 " distance=2.03
    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=0, symmetry=0
  Time building additional restraints: 1.79
  Conformation dependent library (CDL) restraints added in 586.6 milliseconds
  

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2454

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 15 sheets defined
      24.4% alpha, 31.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 189 through 195
    Processing helix  chain 'A' and resid 215 through 232
    Processing helix  chain 'A' and resid 249 through 251
      No H-bonds generated for 'chain 'A' and resid 249 through 251'
    Processing helix  chain 'A' and resid 280 through 288
    Processing helix  chain 'A' and resid 297 through 316
      removed outlier: 3.564A  pdb=" N   LEU A 311 " --> pdb=" O   ASP A 307 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   TYR A 315 " --> pdb=" O   LEU A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 366
      removed outlier: 3.758A  pdb=" N   LEU A 365 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 393
      removed outlier: 4.164A  pdb=" N   GLN A 384 " --> pdb=" O   ASP A 380 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   GLY A 385 " --> pdb=" O   LEU A 381 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   LYS A 386 " --> pdb=" O   VAL A 382 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLU A 387 " --> pdb=" O   ASP A 383 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   GLY A 393 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 552
      removed outlier: 3.817A  pdb=" N   TYR A 548 " --> pdb=" O   ALA A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 651
    Processing helix  chain 'A' and resid 688 through 692
    Processing helix  chain 'A' and resid 726 through 730
    Processing helix  chain 'D' and resid 32 through 45
    Processing helix  chain 'D' and resid 47 through 62
    Processing helix  chain 'D' and resid 67 through 82
    Processing helix  chain 'D' and resid 84 through 99
    Processing helix  chain 'D' and resid 104 through 118
      removed outlier: 3.544A  pdb=" N   VAL D 108 " --> pdb=" O   ASN D 104 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 122 through 128
      removed outlier: 3.698A  pdb=" N   PHE D 128 " --> pdb=" O   LEU D 124 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 131 through 135
      removed outlier: 4.437A  pdb=" N   ASP D 134 " --> pdb=" O   ASP D 131 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 137 through 154
    Processing helix  chain 'D' and resid 159 through 189
      removed outlier: 3.691A  pdb=" N   ASP D 172 " --> pdb=" O   VAL D 168 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   TYR D 177 " --> pdb=" O   ARG D 173 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLU D 178 " --> pdb=" O   LEU D 174 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   GLU D 187 " --> pdb=" O   GLU D 183 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ARG D 188 " --> pdb=" O   TYR D 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 205
    Processing helix  chain 'D' and resid 208 through 225
      removed outlier: 3.749A  pdb=" N   ARG D 212 " --> pdb=" O   THR D 208 " (cutoff:3.500A)
      Proline residue:  D 216  - end of helix
      removed outlier: 3.554A  pdb=" N   MET D 225 " --> pdb=" O   ALA D 221 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 227 through 241
      removed outlier: 3.855A  pdb=" N   LYS D 233 " --> pdb=" O   ALA D 229 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 39 through 44
      removed outlier: 3.811A  pdb=" N   ALA C  44 " --> pdb=" O   TYR C  41 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 80
    Processing helix  chain 'E' and resid 23 through 27
      removed outlier: 3.831A  pdb=" N   VAL E  26 " --> pdb=" O   LEU E  23 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 39 through 44
    Processing helix  chain 'E' and resid 51 through 60
    Processing helix  chain 'E' and resid 81 through 84
    Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 183
      removed outlier: 7.995A  pdb=" N   VAL A 256 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   ILE A 180 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   VAL A 258 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 5.065A  pdb=" N   ILE A 182 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   ILE A 260 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   SER A 242 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   THR A 261 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 5.518A  pdb=" N   ILE A 240 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 276
      removed outlier: 6.224A  pdb=" N   LYS A 267 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   LEU A 337 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
      removed outlier: 8.388A  pdb=" N   SER A 269 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 12.422A  pdb=" N   VAL A 339 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
      removed outlier: 9.628A  pdb=" N   VAL A 271 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 11.726A  pdb=" N   VAL A 341 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 9.780A  pdb=" N   VAL A 273 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 355
      removed outlier: 6.240A  pdb=" N   TYR A 348 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   VAL A 414 " --> pdb=" O   TYR A 348 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   ARG A 350 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 12.759A  pdb=" N   TYR A 416 " --> pdb=" O   ARG A 350 " (cutoff:3.500A)
      removed outlier: 10.055A  pdb=" N   ILE A 352 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 12.338A  pdb=" N   VAL A 418 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
      removed outlier: 9.920A  pdb=" N   PHE A 354 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 11.940A  pdb=" N   GLU A 420 " --> pdb=" O   PHE A 354 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   LYS A 417 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   VAL A 398 " --> pdb=" O   LYS A 417 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   LYS A 419 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 355
      removed outlier: 6.240A  pdb=" N   TYR A 348 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   VAL A 414 " --> pdb=" O   TYR A 348 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   ARG A 350 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 12.759A  pdb=" N   TYR A 416 " --> pdb=" O   ARG A 350 " (cutoff:3.500A)
      removed outlier: 10.055A  pdb=" N   ILE A 352 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 12.338A  pdb=" N   VAL A 418 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
      removed outlier: 9.920A  pdb=" N   PHE A 354 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 11.940A  pdb=" N   GLU A 420 " --> pdb=" O   PHE A 354 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 802 through 805
      removed outlier: 3.601A  pdb=" N   ALA A 770 " --> pdb=" O   GLN A 789 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   PHE A 791 " --> pdb=" O   MET A 768 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   MET A 768 " --> pdb=" O   PHE A 791 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 5.807A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 33 through 35
      removed outlier: 3.926A  pdb=" N   MET E  64 " --> pdb=" O   PHE E  74 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 33 through 35
      removed outlier: 6.689A  pdb=" N   THR E  90 " --> pdb=" O   ASN E 106 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   ASN E 106 " --> pdb=" O   THR E  90 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   THR E  92 " --> pdb=" O   ILE E 104 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   ILE E 104 " --> pdb=" O   THR E  92 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   THR E  94 " --> pdb=" O   THR E 102 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 48 through 50
    Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 68
      removed outlier: 5.918A  pdb=" N   ASN B  85 " --> pdb=" O   GLU B  91 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   GLU B  91 " --> pdb=" O   ASN B  85 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 111 through 118
      removed outlier: 6.307A  pdb=" N   GLY B 114 " --> pdb=" O   TYR B 123 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   TYR B 123 " --> pdb=" O   GLY B 114 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   THR B 116 " --> pdb=" O   HIS B 121 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   HIS B 121 " --> pdb=" O   THR B 116 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   GLN B 130 " --> pdb=" O   SER B 126 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   ASN B 135 " --> pdb=" O   VAL B 141 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   VAL B 141 " --> pdb=" O   ASN B 135 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158
      removed outlier: 6.625A  pdb=" N   LEU B 171 " --> pdb=" O   THR B 184 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   THR B 184 " --> pdb=" O   LEU B 171 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ALA B 173 " --> pdb=" O   LYS B 182 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203
      removed outlier: 6.833A  pdb=" N   VAL B 216 " --> pdb=" O   GLN B 229 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   GLN B 229 " --> pdb=" O   VAL B 216 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ALA B 218 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254
      removed outlier: 6.701A  pdb=" N   LEU B 267 " --> pdb=" O   LYS B 280 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   LYS B 280 " --> pdb=" O   LEU B 267 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ALA B 269 " --> pdb=" O   MET B 278 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292
      removed outlier: 6.735A  pdb=" N   VAL B 305 " --> pdb=" O   THR B 318 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   THR B 318 " --> pdb=" O   VAL B 305 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   ALA B 307 " --> pdb=" O   LEU B 316 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333
      removed outlier: 6.870A  pdb=" N   LEU B 346 " --> pdb=" O   GLN B 359 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   GLN B 359 " --> pdb=" O   LEU B 346 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   TRP B 348 " --> pdb=" O   VAL B 357 " (cutoff:3.500A)

    471 hydrogen bonds defined for protein.
    1281 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: 5.33

  Time building geometry restraints manager: 2.51 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: 10107
        1.03 -     1.23: 15
        1.23 -     1.42: 4663
        1.42 -     1.62: 6018
        1.62 -     1.81: 60
  Bond restraints: 20863
  Sorted by residual:
  bond pdb=" CB  TRP A 376 "
       pdb=" CG  TRP A 376 "
    ideal  model  delta    sigma   weight residual
    1.498  1.458  0.040 3.10e-02 1.04e+03 1.67e+00
  bond pdb=" CB  PHE A 354 "
       pdb=" CG  PHE A 354 "
    ideal  model  delta    sigma   weight residual
    1.502  1.475  0.027 2.30e-02 1.89e+03 1.34e+00
  bond pdb=" CB  ARG D 197 "
       pdb=" CG  ARG D 197 "
    ideal  model  delta    sigma   weight residual
    1.520  1.488  0.032 3.00e-02 1.11e+03 1.17e+00
  bond pdb=" CB  PHE A 738 "
       pdb=" CG  PHE A 738 "
    ideal  model  delta    sigma   weight residual
    1.502  1.478  0.024 2.30e-02 1.89e+03 1.08e+00
  bond pdb=" CA  TYR A 348 "
       pdb=" CB  TYR A 348 "
    ideal  model  delta    sigma   weight residual
    1.534  1.510  0.024 2.33e-02 1.84e+03 1.06e+00
  ... (remaining 20858 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.19: 34586
        1.19 -     2.38: 2600
        2.38 -     3.56: 234
        3.56 -     4.75: 57
        4.75 -     5.94: 8
  Bond angle restraints: 37485
  Sorted by residual:
  angle pdb=" C   TYR D 185 "
        pdb=" N   THR D 186 "
        pdb=" CA  THR D 186 "
      ideal   model   delta    sigma   weight residual
     120.72  115.65    5.07 1.67e+00 3.59e-01 9.22e+00
  angle pdb=" N   ASP D 204 "
        pdb=" CA  ASP D 204 "
        pdb=" C   ASP D 204 "
      ideal   model   delta    sigma   weight residual
     112.90  116.87   -3.97 1.31e+00 5.83e-01 9.18e+00
  angle pdb=" N   ASN E 103 "
        pdb=" CA  ASN E 103 "
        pdb=" C   ASN E 103 "
      ideal   model   delta    sigma   weight residual
     108.99  113.65   -4.66 1.57e+00 4.06e-01 8.82e+00
  angle pdb=" C   ARG P1297 "
        pdb=" N   TYR P1298 "
        pdb=" CA  TYR P1298 "
      ideal   model   delta    sigma   weight residual
     122.81  127.32   -4.51 1.57e+00 4.06e-01 8.25e+00
  angle pdb=" N   LEU B 192 "
        pdb=" CA  LEU B 192 "
        pdb=" C   LEU B 192 "
      ideal   model   delta    sigma   weight residual
     110.80  116.74   -5.94 2.13e+00 2.20e-01 7.78e+00
  ... (remaining 37480 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.89: 9324
       16.89 -    33.78: 341
       33.78 -    50.67: 161
       50.67 -    67.57: 78
       67.57 -    84.46: 10
  Dihedral angle restraints: 9914
    sinusoidal: 5319
      harmonic: 4595
  Sorted by residual:
  dihedral pdb=" CA  ASN A 422 "
           pdb=" C   ASN A 422 "
           pdb=" N   THR A 423 "
           pdb=" CA  THR A 423 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.91  -21.09     0      5.00e+00 4.00e-02 1.78e+01
  dihedral pdb=" CA  LEU B 298 "
           pdb=" C   LEU B 298 "
           pdb=" N   VAL B 299 "
           pdb=" CA  VAL B 299 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.07   18.93     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  LEU B 192 "
           pdb=" C   LEU B 192 "
           pdb=" N   SER B 193 "
           pdb=" CA  SER B 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.54  -18.46     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 9911 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1033
       0.038 -    0.075: 372
       0.075 -    0.113: 134
       0.113 -    0.150: 40
       0.150 -    0.188: 4
  Chirality restraints: 1583
  Sorted by residual:
  chirality pdb=" CA  TYR D 185 "
            pdb=" N   TYR D 185 "
            pdb=" C   TYR D 185 "
            pdb=" CB  TYR D 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.83e-01
  chirality pdb=" CA  ARG A 366 "
            pdb=" N   ARG A 366 "
            pdb=" C   ARG A 366 "
            pdb=" CB  ARG A 366 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.27e-01
  chirality pdb=" CA  ARG D 141 "
            pdb=" N   ARG D 141 "
            pdb=" C   ARG D 141 "
            pdb=" CB  ARG D 141 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.15e-01
  ... (remaining 1580 not shown)

  Planarity restraints: 3203
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 282 "    0.015 2.00e-02 2.50e+03   3.03e-02 9.17e+00
        pdb=" C   ALA A 282 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   ALA A 282 "    0.020 2.00e-02 2.50e+03
        pdb=" N   GLU A 283 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO D  86 "    0.013 2.00e-02 2.50e+03   2.51e-02 6.30e+00
        pdb=" C   PRO D  86 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   PRO D  86 "    0.016 2.00e-02 2.50e+03
        pdb=" N   LEU D  87 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 136 "   -0.041 5.00e-02 4.00e+02   6.20e-02 6.14e+00
        pdb=" N   PRO D 137 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO D 137 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO D 137 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 3200 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.15: 661
        2.15 -     2.76: 38966
        2.76 -     3.38: 53372
        3.38 -     3.99: 69854
        3.99 -     4.60: 109055
  Nonbonded interactions: 271908
  Sorted by model distance:
  nonbonded pdb=" HZ3 LYS A 310 "
            pdb=" OD1 ASP A 380 "
     model   vdw
     1.541 2.450
  nonbonded pdb=" HG  SER A 360 "
            pdb=" OE2 GLU A 420 "
     model   vdw
     1.550 2.450
  nonbonded pdb=" OD1 ASP D 134 "
            pdb=" HG  SER D 180 "
     model   vdw
     1.558 2.450
  nonbonded pdb=" H   ILE A 352 "
            pdb=" OE2 GLU A 373 "
     model   vdw
     1.562 2.450
  nonbonded pdb=" H   ASP A 568 "
            pdb=" OD2 ASP A 605 "
     model   vdw
     1.569 2.450
  ... (remaining 271903 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:             1.280
  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:             0.110
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     20.060
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
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      :  0.005   0.040  10758  Z= 0.220
  Angle     :  0.774   5.942  14617  Z= 0.465
  Chirality :  0.046   0.188   1583
  Planarity :  0.005   0.062   1925
  Dihedral  : 10.614  84.456   3877
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  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 are not related in a simple way.
  whole:  0.72 (0.22), residues: 1322
  helix:  0.34 (0.28), residues: 278
  sheet:  0.95 (0.24), residues: 430
  loop :  0.35 (0.25), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.029   0.001   ARG A 734 
 TYR   0.021   0.002   TYR D 177 
 PHE   0.010   0.002   PHE A 586 
 TRP   0.028   0.003   TRP A 576 
 HIS   0.007   0.001   HIS B 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (10756)
  covalent geometry    : angle       0.77372 (14613)
  SS BOND              : bond        0.00306 (    2)
  SS BOND              : angle       1.62991 (    4)
  hydrogen bonds       : bond        0.11509 (  469)
  hydrogen bonds       : angle       6.78690 ( 1281)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  410 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 410
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7437 (mt-10)
REVERT: A  768 MET cc_start: 0.8555 (mtt) cc_final: 0.8219 (mtm)
REVERT: D   56 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8359 (tm-30)
REVERT: D   60 ASN cc_start: 0.8802 (m-40) cc_final: 0.8444 (m110)
REVERT: D   82 ASN cc_start: 0.7879 (t0) cc_final: 0.7527 (t0)
REVERT: C   41 TYR cc_start: 0.8158 (p90) cc_final: 0.7939 (p90)
REVERT: C   42 LEU cc_start: 0.8906 (mt) cc_final: 0.8184 (tp)
REVERT: E   31 ASP cc_start: 0.8453 (m-30) cc_final: 0.8006 (p0)
REVERT: E  101 LEU cc_start: 0.8035 (tp) cc_final: 0.7759 (tp)
REVERT: B  157 VAL cc_start: 0.8625 (t) cc_final: 0.7958 (t)
REVERT: B  343 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7631 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 410
  average time/residue: 0.2370
  time to fit residues: 132.4057
Evaluate side-chains
  265 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 265
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:    0.0050
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    0.0970
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.8198

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

Flipped N/Q/H residues before XYZ refinement:
A 259 ASN
A 276 ASN
A 446 GLN
** D  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 138 GLN
** C  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 121 HIS
B 168 ASN
** B 172 GLN ** 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 = 0.4004 r_free = 0.4004 target = 0.161319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.110758 restraints weight = 57237.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.116503 restraints weight = 27745.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.120336 restraints weight = 18074.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.122613 restraints weight = 14006.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.124026 restraints weight = 12085.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.3285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.141  10758  Z= 0.195
  Angle     :  0.619  17.526  14617  Z= 0.344
  Chirality :  0.045   0.358   1583
  Planarity :  0.005   0.056   1925
  Dihedral  :  4.876  39.000   1475
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.89 %
    Favored  : 99.02 %
  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 are not related in a simple way.
  whole:  0.93 (0.22), residues: 1322
  helix:  1.40 (0.30), residues: 286
  sheet:  0.65 (0.24), residues: 432
  loop :  0.35 (0.25), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 734 
 TYR   0.015   0.002   TYR D  79 
 PHE   0.019   0.002   PHE A 737 
 TRP   0.016   0.002   TRP A 576 
 HIS   0.004   0.001   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 (10756)
  covalent geometry    : angle       0.61107 (14613)
  SS BOND              : bond        0.01593 (    2)
  SS BOND              : angle       5.86967 (    4)
  hydrogen bonds       : bond        0.05394 (  469)
  hydrogen bonds       : angle       5.96630 ( 1281)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 298
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 ILE cc_start: 0.9518 (mt) cc_final: 0.9218 (tt)
REVERT: A  287 LEU cc_start: 0.8410 (mt) cc_final: 0.8172 (mt)
REVERT: A  420 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7693 (mt-10)
REVERT: A  545 MET cc_start: 0.9061 (mtm) cc_final: 0.8698 (mtm)
REVERT: A  709 ASN cc_start: 0.8668 (m110) cc_final: 0.8407 (m110)
REVERT: A  738 PHE cc_start: 0.8598 (p90) cc_final: 0.8397 (p90)
REVERT: D   82 ASN cc_start: 0.8405 (t0) cc_final: 0.7973 (t0)
REVERT: D  242 SER cc_start: 0.8166 (m) cc_final: 0.7946 (p)
REVERT: C   81 ASP cc_start: 0.8154 (t0) cc_final: 0.7820 (t0)
REVERT: E   31 ASP cc_start: 0.8598 (m-30) cc_final: 0.8252 (p0)
REVERT: E  103 ASN cc_start: 0.8311 (t0) cc_final: 0.8014 (m110)
REVERT: B   76 ASP cc_start: 0.8132 (t0) cc_final: 0.7865 (t0)
REVERT: B   82 LYS cc_start: 0.7850 (mtmt) cc_final: 0.7626 (mtmt)
REVERT: B  150 GLU cc_start: 0.8513 (mp0) cc_final: 0.8184 (mp0)
REVERT: B  153 SER cc_start: 0.8600 (t) cc_final: 0.8298 (t)
REVERT: B  303 ASP cc_start: 0.7922 (m-30) cc_final: 0.6579 (m-30)
REVERT: B  327 LEU cc_start: 0.8087 (mt) cc_final: 0.7613 (mt)
REVERT: B  343 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7665 (mp0)
  outliers start: 1
  outliers final: 0
  residues processed: 299
  average time/residue: 0.2422
  time to fit residues: 98.7421
Evaluate side-chains
  251 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 126 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 117 optimal weight:   10.0000
   chunk 72 optimal weight:    3.9990
   chunk 116 optimal weight:    4.9990
   chunk 107 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9990
   chunk 101 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
A 606 ASN
** D  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 116 ASN
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  51 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 = 0.4002 r_free = 0.4002 target = 0.161069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.121550 restraints weight = 57982.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.125781 restraints weight = 42681.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.127329 restraints weight = 29488.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.128165 restraints weight = 20497.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.132417 restraints weight = 18330.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.3943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  10758  Z= 0.178
  Angle     :  0.562  13.579  14617  Z= 0.310
  Chirality :  0.044   0.277   1583
  Planarity :  0.004   0.044   1925
  Dihedral  :  4.721  38.735   1475
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.07 %
    Favored  : 98.84 %
  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 are not related in a simple way.
  whole:  0.70 (0.22), residues: 1322
  helix:  1.41 (0.30), residues: 286
  sheet:  0.29 (0.23), residues: 428
  loop :  0.28 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 295 
 TYR   0.026   0.001   TYR D  79 
 PHE   0.014   0.001   PHE A 238 
 TRP   0.012   0.001   TRP B 317 
 HIS   0.005   0.001   HIS B 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (10756)
  covalent geometry    : angle       0.55824 (14613)
  SS BOND              : bond        0.01580 (    2)
  SS BOND              : angle       4.07057 (    4)
  hydrogen bonds       : bond        0.04718 (  469)
  hydrogen bonds       : angle       5.62976 ( 1281)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 267
  time to evaluate  : 0.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 ILE cc_start: 0.9429 (mt) cc_final: 0.9210 (tt)
REVERT: A  287 LEU cc_start: 0.8247 (mt) cc_final: 0.8003 (mt)
REVERT: A  709 ASN cc_start: 0.8550 (m110) cc_final: 0.8324 (m110)
REVERT: A  741 MET cc_start: 0.7613 (ptm) cc_final: 0.7352 (ptt)
REVERT: A  787 TYR cc_start: 0.7270 (t80) cc_final: 0.6722 (t80)
REVERT: D   82 ASN cc_start: 0.8421 (t0) cc_final: 0.8017 (t0)
REVERT: D  207 ASP cc_start: 0.7230 (p0) cc_final: 0.7026 (p0)
REVERT: D  242 SER cc_start: 0.8437 (m) cc_final: 0.8229 (p)
REVERT: C   81 ASP cc_start: 0.8103 (t0) cc_final: 0.7812 (t0)
REVERT: E   31 ASP cc_start: 0.8610 (m-30) cc_final: 0.8302 (p0)
REVERT: E  103 ASN cc_start: 0.8336 (t0) cc_final: 0.8054 (m110)
REVERT: B   76 ASP cc_start: 0.8026 (t0) cc_final: 0.7672 (t0)
REVERT: B   82 LYS cc_start: 0.7720 (mttt) cc_final: 0.7428 (mtmt)
REVERT: B  189 MET cc_start: 0.8586 (pmm) cc_final: 0.7443 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 268
  average time/residue: 0.2236
  time to fit residues: 83.7932
Evaluate side-chains
  231 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 106 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   chunk 53 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 116 optimal weight:    5.9990
   chunk 67 optimal weight:    7.9990
   chunk 45 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 186 HIS
A 276 ASN
D 116 ASN
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 121 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.158733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.107955 restraints weight = 57664.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.113655 restraints weight = 28038.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.117336 restraints weight = 18229.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.119591 restraints weight = 14157.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.120840 restraints weight = 12210.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.4366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073  10758  Z= 0.191
  Angle     :  0.554  12.414  14617  Z= 0.305
  Chirality :  0.043   0.230   1583
  Planarity :  0.004   0.045   1925
  Dihedral  :  4.658  39.529   1475
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.16 %
    Favored  : 98.75 %
  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 are not related in a simple way.
  whole:  0.47 (0.23), residues: 1322
  helix:  1.21 (0.30), residues: 286
  sheet:  0.23 (0.24), residues: 418
  loop :  0.08 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 388 
 TYR   0.017   0.002   TYR D  79 
 PHE   0.012   0.001   PHE A 426 
 TRP   0.012   0.001   TRP B 317 
 HIS   0.014   0.001   HIS B 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 (10756)
  covalent geometry    : angle       0.55060 (14613)
  SS BOND              : bond        0.01361 (    2)
  SS BOND              : angle       3.58448 (    4)
  hydrogen bonds       : bond        0.04457 (  469)
  hydrogen bonds       : angle       5.54866 ( 1281)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 265
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: 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  180 ILE cc_start: 0.9468 (mt) cc_final: 0.9232 (tt)
REVERT: A  222 ASP cc_start: 0.8722 (m-30) cc_final: 0.8517 (m-30)
REVERT: A  420 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7560 (mt-10)
REVERT: A  709 ASN cc_start: 0.8589 (m110) cc_final: 0.8255 (m110)
REVERT: A  741 MET cc_start: 0.7780 (ptm) cc_final: 0.7543 (ptt)
REVERT: A  787 TYR cc_start: 0.7294 (t80) cc_final: 0.6808 (t80)
REVERT: D   82 ASN cc_start: 0.8594 (t0) cc_final: 0.8081 (t0)
REVERT: D  242 SER cc_start: 0.8230 (m) cc_final: 0.8008 (p)
REVERT: C   81 ASP cc_start: 0.8147 (t0) cc_final: 0.7825 (t0)
REVERT: E  103 ASN cc_start: 0.8184 (t0) cc_final: 0.7931 (m110)
REVERT: B   76 ASP cc_start: 0.8037 (t0) cc_final: 0.7747 (t0)
REVERT: B   82 LYS cc_start: 0.7998 (mttt) cc_final: 0.7638 (mtmt)
REVERT: B  127 GLU cc_start: 0.8155 (mp0) cc_final: 0.7876 (mp0)
REVERT: B  161 LEU cc_start: 0.8913 (mm) cc_final: 0.8656 (mm)
REVERT: B  189 MET cc_start: 0.8616 (pmm) cc_final: 0.7591 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 266
  average time/residue: 0.2256
  time to fit residues: 83.0638
Evaluate side-chains
  230 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 104 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 119 optimal weight:    9.9990
   chunk 18 optimal weight:    0.9990
   chunk 67 optimal weight:    9.9990
   chunk 111 optimal weight:    8.9990
   chunk 32 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
A 651 ASN
D 116 ASN
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  51 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 = 0.3950 r_free = 0.3950 target = 0.156869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.105649 restraints weight = 55095.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.110945 restraints weight = 26940.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.114434 restraints weight = 17686.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.116575 restraints weight = 13802.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.117634 restraints weight = 11947.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.4751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  10758  Z= 0.175
  Angle     :  0.536  11.343  14617  Z= 0.294
  Chirality :  0.043   0.209   1583
  Planarity :  0.004   0.041   1925
  Dihedral  :  4.617  39.728   1475
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.80 %
    Favored  : 99.11 %
  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 are not related in a simple way.
  whole:  0.36 (0.23), residues: 1322
  helix:  1.22 (0.30), residues: 286
  sheet:  0.13 (0.24), residues: 418
  loop : -0.02 (0.26), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 304 
 TYR   0.013   0.001   TYR A 348 
 PHE   0.027   0.002   PHE A 238 
 TRP   0.012   0.001   TRP B 317 
 HIS   0.015   0.001   HIS B 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (10756)
  covalent geometry    : angle       0.53323 (14613)
  SS BOND              : bond        0.01261 (    2)
  SS BOND              : angle       3.34490 (    4)
  hydrogen bonds       : bond        0.04264 (  469)
  hydrogen bonds       : angle       5.42545 ( 1281)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 261
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: 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  180 ILE cc_start: 0.9462 (mt) cc_final: 0.9234 (tt)
REVERT: A  222 ASP cc_start: 0.8688 (m-30) cc_final: 0.8381 (m-30)
REVERT: A  373 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7918 (mt-10)
REVERT: A  420 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7512 (mt-10)
REVERT: A  709 ASN cc_start: 0.8498 (m110) cc_final: 0.8168 (m110)
REVERT: A  787 TYR cc_start: 0.7415 (t80) cc_final: 0.6894 (t80)
REVERT: D   82 ASN cc_start: 0.8479 (t0) cc_final: 0.8071 (t0)
REVERT: D  242 SER cc_start: 0.8269 (m) cc_final: 0.8051 (p)
REVERT: C   81 ASP cc_start: 0.8156 (t0) cc_final: 0.7857 (t0)
REVERT: B   76 ASP cc_start: 0.8080 (t0) cc_final: 0.7755 (t0)
REVERT: B   82 LYS cc_start: 0.8044 (mttt) cc_final: 0.7740 (mtmt)
REVERT: B  127 GLU cc_start: 0.8303 (mp0) cc_final: 0.8061 (mp0)
REVERT: B  161 LEU cc_start: 0.8899 (mm) cc_final: 0.8643 (mm)
REVERT: B  189 MET cc_start: 0.8655 (pmm) cc_final: 0.7578 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 262
  average time/residue: 0.2294
  time to fit residues: 83.6467
Evaluate side-chains
  226 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 97 optimal weight:    8.9990
   chunk 7 optimal weight:    3.9990
   chunk 128 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0020
   chunk 118 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 67 optimal weight:   10.0000
   overall best weight:    0.7392

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
D 116 ASN
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.158342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.118863 restraints weight = 54700.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.122281 restraints weight = 37847.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.123011 restraints weight = 31148.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.125466 restraints weight = 18651.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.126350 restraints weight = 15496.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.4906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.060  10758  Z= 0.108
  Angle     :  0.496  10.446  14617  Z= 0.269
  Chirality :  0.043   0.189   1583
  Planarity :  0.003   0.036   1925
  Dihedral  :  4.419  37.253   1475
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.89 %
    Favored  : 99.02 %
  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 are not related in a simple way.
  whole:  0.54 (0.23), residues: 1322
  helix:  1.54 (0.30), residues: 285
  sheet:  0.24 (0.24), residues: 417
  loop :  0.01 (0.26), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 304 
 TYR   0.014   0.001   TYR C  41 
 PHE   0.017   0.001   PHE A 238 
 TRP   0.008   0.001   TRP A 576 
 HIS   0.004   0.001   HIS B 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (10756)
  covalent geometry    : angle       0.49409 (14613)
  SS BOND              : bond        0.01104 (    2)
  SS BOND              : angle       2.91279 (    4)
  hydrogen bonds       : bond        0.03846 (  469)
  hydrogen bonds       : angle       5.15029 ( 1281)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 261
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: 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  180 ILE cc_start: 0.9418 (mt) cc_final: 0.9207 (tt)
REVERT: A  222 ASP cc_start: 0.8493 (m-30) cc_final: 0.8255 (m-30)
REVERT: A  272 GLU cc_start: 0.7883 (tp30) cc_final: 0.7605 (tp30)
REVERT: A  420 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7668 (mt-10)
REVERT: A  741 MET cc_start: 0.7474 (ptm) cc_final: 0.7219 (ptt)
REVERT: A  765 ASN cc_start: 0.8647 (m-40) cc_final: 0.8360 (m-40)
REVERT: A  787 TYR cc_start: 0.7373 (t80) cc_final: 0.6897 (t80)
REVERT: D   56 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8224 (tm-30)
REVERT: D   82 ASN cc_start: 0.8329 (t0) cc_final: 0.7992 (t0)
REVERT: D  242 SER cc_start: 0.8602 (m) cc_final: 0.8385 (p)
REVERT: C   81 ASP cc_start: 0.8136 (t0) cc_final: 0.7814 (t0)
REVERT: C   82 ILE cc_start: 0.8884 (pt) cc_final: 0.8575 (pt)
REVERT: B   76 ASP cc_start: 0.8156 (t0) cc_final: 0.7861 (t0)
REVERT: B   82 LYS cc_start: 0.7736 (mttt) cc_final: 0.7481 (mtmt)
REVERT: B  189 MET cc_start: 0.8645 (pmm) cc_final: 0.7893 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 262
  average time/residue: 0.2397
  time to fit residues: 87.2719
Evaluate side-chains
  226 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 103 optimal weight:    5.9990
   chunk 99 optimal weight:    5.9990
   chunk 76 optimal weight:    3.9990
   chunk 120 optimal weight:   10.0000
   chunk 108 optimal weight:    3.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
A 573 ASN
D 116 ASN
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  51 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 = 0.3933 r_free = 0.3933 target = 0.155523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.104379 restraints weight = 55607.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.109593 restraints weight = 27791.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.113013 restraints weight = 18429.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.115016 restraints weight = 14468.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.116307 restraints weight = 12591.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.5151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  10758  Z= 0.214
  Angle     :  0.545   9.542  14617  Z= 0.300
  Chirality :  0.043   0.188   1583
  Planarity :  0.004   0.046   1925
  Dihedral  :  4.553  38.957   1475
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.54 %
    Favored  : 99.38 %
  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 are not related in a simple way.
  whole:  0.25 (0.23), residues: 1322
  helix:  1.38 (0.30), residues: 285
  sheet:  0.05 (0.24), residues: 412
  loop : -0.21 (0.26), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 195 
 TYR   0.018   0.002   TYR A 348 
 PHE   0.020   0.002   PHE A 238 
 TRP   0.017   0.001   TRP B 317 
 HIS   0.006   0.001   HIS B 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (10756)
  covalent geometry    : angle       0.54280 (14613)
  SS BOND              : bond        0.01051 (    2)
  SS BOND              : angle       2.68474 (    4)
  hydrogen bonds       : bond        0.04148 (  469)
  hydrogen bonds       : angle       5.35631 ( 1281)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 252
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: 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: 0.8729 (m-30) cc_final: 0.8405 (m-30)
REVERT: A  231 LEU cc_start: 0.9263 (mt) cc_final: 0.9051 (mt)
REVERT: A  272 GLU cc_start: 0.7959 (tp30) cc_final: 0.7621 (tp30)
REVERT: A  420 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7582 (mt-10)
REVERT: A  741 MET cc_start: 0.7612 (ptm) cc_final: 0.7329 (ptt)
REVERT: A  787 TYR cc_start: 0.7492 (t80) cc_final: 0.6945 (t80)
REVERT: D   56 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8285 (tm-30)
REVERT: D   82 ASN cc_start: 0.8475 (t0) cc_final: 0.8075 (t0)
REVERT: C   81 ASP cc_start: 0.8135 (t0) cc_final: 0.7830 (t0)
REVERT: B   76 ASP cc_start: 0.8044 (t0) cc_final: 0.7704 (t0)
REVERT: B   82 LYS cc_start: 0.8007 (mttt) cc_final: 0.7778 (mtmt)
REVERT: B  127 GLU cc_start: 0.8295 (mp0) cc_final: 0.8039 (mp0)
REVERT: B  189 MET cc_start: 0.8933 (pmm) cc_final: 0.7757 (pmm)
REVERT: B  300 ASP cc_start: 0.8563 (t0) cc_final: 0.8241 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 253
  average time/residue: 0.2276
  time to fit residues: 80.2633
Evaluate side-chains
  222 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 83 optimal weight:    3.9990
   chunk 126 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 64 optimal weight:   10.0000
   chunk 115 optimal weight:    7.9990
   chunk 108 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 113 optimal weight:    0.8980
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
A 765 ASN
D  41 GLN
D 116 ASN
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 GLN ** 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 = 0.3910 r_free = 0.3910 target = 0.153600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.102805 restraints weight = 55718.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.107905 restraints weight = 28105.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.111175 restraints weight = 18705.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.113275 restraints weight = 14750.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.114508 restraints weight = 12800.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.5388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055  10758  Z= 0.252
  Angle     :  0.588   9.469  14617  Z= 0.325
  Chirality :  0.044   0.196   1583
  Planarity :  0.004   0.073   1925
  Dihedral  :  4.760  41.950   1475
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.80 %
    Favored  : 99.11 %
  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 are not related in a simple way.
  whole: -0.16 (0.23), residues: 1322
  helix:  1.08 (0.30), residues: 285
  sheet: -0.07 (0.24), residues: 402
  loop : -0.61 (0.25), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  97 
 TYR   0.024   0.002   TYR A 348 
 PHE   0.014   0.002   PHE A 426 
 TRP   0.013   0.002   TRP B 317 
 HIS   0.018   0.002   HIS B 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00551 (10756)
  covalent geometry    : angle       0.58606 (14613)
  SS BOND              : bond        0.01104 (    2)
  SS BOND              : angle       2.77674 (    4)
  hydrogen bonds       : bond        0.04402 (  469)
  hydrogen bonds       : angle       5.52630 ( 1281)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 242
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ASP cc_start: 0.8716 (m-30) cc_final: 0.8437 (m-30)
REVERT: A  272 GLU cc_start: 0.8071 (tp30) cc_final: 0.7706 (tp30)
REVERT: A  420 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7644 (mt-10)
REVERT: A  445 GLN cc_start: 0.7777 (tt0) cc_final: 0.7572 (tt0)
REVERT: A  741 MET cc_start: 0.7686 (ptm) cc_final: 0.7412 (ptt)
REVERT: A  787 TYR cc_start: 0.7449 (t80) cc_final: 0.6755 (t80)
REVERT: D   56 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8264 (tm-30)
REVERT: D   82 ASN cc_start: 0.8533 (t0) cc_final: 0.8117 (t0)
REVERT: C   81 ASP cc_start: 0.8138 (t0) cc_final: 0.7921 (t0)
REVERT: B   76 ASP cc_start: 0.8012 (t0) cc_final: 0.7672 (t0)
REVERT: B   82 LYS cc_start: 0.8027 (mttt) cc_final: 0.7675 (mtmt)
REVERT: B  127 GLU cc_start: 0.8377 (mp0) cc_final: 0.8071 (mp0)
REVERT: B  189 MET cc_start: 0.9016 (pmm) cc_final: 0.7925 (pmm)
REVERT: B  300 ASP cc_start: 0.8557 (t0) cc_final: 0.8192 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 243
  average time/residue: 0.2453
  time to fit residues: 82.3618
Evaluate side-chains
  210 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 105 optimal weight:    5.9990
   chunk 95 optimal weight:    3.9990
   chunk 66 optimal weight:    9.9990
   chunk 98 optimal weight:   10.0000
   chunk 48 optimal weight:    3.9990
   chunk 123 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 42 optimal weight:    0.6980
   chunk 21 optimal weight:    0.3980
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
D 116 ASN
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 121 HIS
** B 172 GLN ** 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 = 0.3921 r_free = 0.3921 target = 0.154486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.103688 restraints weight = 56114.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.108830 restraints weight = 28431.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.112160 restraints weight = 19006.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.114258 restraints weight = 14965.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.115499 restraints weight = 12999.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.5537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10758  Z= 0.190
  Angle     :  0.555   9.106  14617  Z= 0.304
  Chirality :  0.043   0.174   1583
  Planarity :  0.004   0.060   1925
  Dihedral  :  4.713  42.098   1475
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.54 %
    Favored  : 99.38 %
  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 are not related in a simple way.
  whole: -0.15 (0.23), residues: 1322
  helix:  1.15 (0.30), residues: 285
  sheet: -0.09 (0.24), residues: 410
  loop : -0.61 (0.25), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D  97 
 TYR   0.018   0.001   TYR A 348 
 PHE   0.016   0.002   PHE P1296 
 TRP   0.029   0.002   TRP B  93 
 HIS   0.011   0.001   HIS B 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (10756)
  covalent geometry    : angle       0.55321 (14613)
  SS BOND              : bond        0.01014 (    2)
  SS BOND              : angle       2.53307 (    4)
  hydrogen bonds       : bond        0.04184 (  469)
  hydrogen bonds       : angle       5.42064 ( 1281)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 247
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ASP cc_start: 0.8710 (m-30) cc_final: 0.8381 (m-30)
REVERT: A  272 GLU cc_start: 0.8059 (tp30) cc_final: 0.7712 (tp30)
REVERT: A  420 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7593 (mt-10)
REVERT: A  741 MET cc_start: 0.7682 (ptm) cc_final: 0.7410 (ptt)
REVERT: A  787 TYR cc_start: 0.7208 (t80) cc_final: 0.6680 (t80)
REVERT: D   56 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8296 (tm-30)
REVERT: D   82 ASN cc_start: 0.8536 (t0) cc_final: 0.8125 (t0)
REVERT: B   76 ASP cc_start: 0.8049 (t0) cc_final: 0.7689 (t0)
REVERT: B   82 LYS cc_start: 0.8063 (mttt) cc_final: 0.7701 (mtmt)
REVERT: B  127 GLU cc_start: 0.8400 (mp0) cc_final: 0.8072 (mp0)
REVERT: B  189 MET cc_start: 0.8987 (pmm) cc_final: 0.7967 (pmm)
REVERT: B  273 ARG cc_start: 0.9067 (mtp85) cc_final: 0.8828 (mmt90)
REVERT: B  300 ASP cc_start: 0.8522 (t0) cc_final: 0.8115 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 247
  average time/residue: 0.2439
  time to fit residues: 83.5299
Evaluate side-chains
  212 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 105 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 125 optimal weight:    9.9990
   chunk 107 optimal weight:    0.9990
   chunk 127 optimal weight:    9.9990
   chunk 61 optimal weight:    7.9990
   chunk 96 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
D 116 ASN
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 121 HIS
** B 172 GLN ** 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 = 0.3905 r_free = 0.3905 target = 0.153221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.102565 restraints weight = 55321.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.107684 restraints weight = 27743.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.111052 restraints weight = 18333.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.113142 restraints weight = 14350.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.114183 restraints weight = 12402.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.5588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10758  Z= 0.202
  Angle     :  0.551   8.690  14617  Z= 0.304
  Chirality :  0.043   0.169   1583
  Planarity :  0.004   0.042   1925
  Dihedral  :  4.713  42.553   1475
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  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 are not related in a simple way.
  whole: -0.24 (0.23), residues: 1322
  helix:  1.16 (0.30), residues: 284
  sheet: -0.18 (0.24), residues: 415
  loop : -0.68 (0.25), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  97 
 TYR   0.020   0.002   TYR A 348 
 PHE   0.013   0.002   PHE A 440 
 TRP   0.012   0.001   TRP A 635 
 HIS   0.014   0.001   HIS B 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 (10756)
  covalent geometry    : angle       0.54947 (14613)
  SS BOND              : bond        0.00974 (    2)
  SS BOND              : angle       2.46561 (    4)
  hydrogen bonds       : bond        0.04188 (  469)
  hydrogen bonds       : angle       5.41039 ( 1281)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ASP cc_start: 0.8720 (m-30) cc_final: 0.8370 (m-30)
REVERT: A  272 GLU cc_start: 0.8050 (tp30) cc_final: 0.7694 (tp30)
REVERT: A  306 ASP cc_start: 0.8748 (t0) cc_final: 0.8540 (t70)
REVERT: A  382 VAL cc_start: 0.8115 (t) cc_final: 0.7270 (m)
REVERT: A  420 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7620 (mt-10)
REVERT: A  741 MET cc_start: 0.7717 (ptm) cc_final: 0.7432 (ptt)
REVERT: A  787 TYR cc_start: 0.7172 (t80) cc_final: 0.6692 (t80)
REVERT: D   56 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8297 (tm-30)
REVERT: D   82 ASN cc_start: 0.8563 (t0) cc_final: 0.8154 (t0)
REVERT: D   92 ILE cc_start: 0.9257 (mm) cc_final: 0.9031 (mm)
REVERT: B   76 ASP cc_start: 0.8054 (t0) cc_final: 0.7676 (t0)
REVERT: B   82 LYS cc_start: 0.8063 (mttt) cc_final: 0.7753 (mtmt)
REVERT: B  127 GLU cc_start: 0.8477 (mp0) cc_final: 0.8160 (mp0)
REVERT: B  189 MET cc_start: 0.9012 (pmm) cc_final: 0.8016 (pmm)
REVERT: B  300 ASP cc_start: 0.8513 (t0) cc_final: 0.8166 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.2338
  time to fit residues: 79.0190
Evaluate side-chains
  215 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 120 optimal weight:    0.8980
   chunk 127 optimal weight:   10.0000
   chunk 58 optimal weight:    4.9990
   chunk 117 optimal weight:    7.9990
   chunk 103 optimal weight:    8.9990
   chunk 52 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 64 optimal weight:    9.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
D 116 ASN
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 121 HIS
** B 172 GLN ** 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 = 0.3926 r_free = 0.3926 target = 0.154676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.104335 restraints weight = 55582.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.109532 restraints weight = 27809.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.112933 restraints weight = 18386.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.114704 restraints weight = 14395.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.116226 restraints weight = 12569.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.5671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10758  Z= 0.167
  Angle     :  0.545  11.243  14617  Z= 0.295
  Chirality :  0.043   0.157   1583
  Planarity :  0.004   0.081   1925
  Dihedral  :  4.657  41.970   1475
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  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 are not related in a simple way.
  whole: -0.19 (0.23), residues: 1322
  helix:  1.17 (0.31), residues: 284
  sheet: -0.12 (0.24), residues: 407
  loop : -0.66 (0.25), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D  97 
 TYR   0.017   0.001   TYR D  79 
 PHE   0.018   0.001   PHE A 428 
 TRP   0.031   0.001   TRP B 317 
 HIS   0.004   0.001   HIS B 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (10756)
  covalent geometry    : angle       0.54329 (14613)
  SS BOND              : bond        0.00960 (    2)
  SS BOND              : angle       2.27448 (    4)
  hydrogen bonds       : bond        0.04040 (  469)
  hydrogen bonds       : angle       5.33604 ( 1281)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3699.52 seconds
wall clock time: 63 minutes 37.19 seconds (3817.19 seconds total)