Starting phenix.real_space_refine
on Sat Aug 23 07:26:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kao_22778/08_2025/7kao_22778.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kao_22778/08_2025/7kao_22778.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kao_22778/08_2025/7kao_22778.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kao_22778/08_2025/7kao_22778.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kao_22778/08_2025/7kao_22778.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kao_22778/08_2025/7kao_22778.map"
  }
  resolution = 4.0
  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=   0.008 sd=   0.058
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      39      5.16       5
     C    6860      2.51       5
     N    1762      2.21       5
     O    1841      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10502
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3369
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 441, 3369
          Classifications: {'peptide': 441}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 20, 'TRANS': 420}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 77
          Unresolved non-hydrogen angles: 96
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'ASP:plan': 3, 'TYR:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 61
    Chain: "C"
      Number of atoms: 435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 435
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 2, 'TRANS': 52}
    Chain: "B"
      Number of atoms: 229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 229
          Classifications: {'peptide': 32}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 30}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "D"
      Number of atoms: 3869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 493, 3869
          Classifications: {'peptide': 493}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 28, 'TRANS': 464}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 99
          Unresolved non-hydrogen angles: 125
          Unresolved non-hydrogen dihedrals: 75
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 12, 'GLN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 86
    Chain: "E"
      Number of atoms: 1129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1129
          Classifications: {'peptide': 138}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 2, 'TRANS': 135}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "F"
      Number of atoms: 1471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1471
          Classifications: {'peptide': 190}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 7, 'TRANS': 182}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
  Time building chain proxies: 2.43, per 1000 atoms: 0.23
  Number of scatterers: 10502
  At special positions: 0
  Unit cell: (108.1, 126.5, 134.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      39     16.00
     O    1841      8.00
     N    1762      7.00
     C    6860      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.94
  Conformation dependent library (CDL) restraints added in 264.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2544

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 6 sheets defined
      67.6% alpha, 4.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 46
    Processing helix  chain 'A' and resid 63 through 70
    Processing helix  chain 'A' and resid 82 through 98
    Processing helix  chain 'A' and resid 107 through 137
      removed outlier: 3.955A  pdb=" N   ARG A 111 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LYS A 119 " --> pdb=" O   GLN A 115 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE A 124 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 174
      removed outlier: 3.766A  pdb=" N   GLY A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 196
    Processing helix  chain 'A' and resid 213 through 225
    Processing helix  chain 'A' and resid 227 through 238
      removed outlier: 4.457A  pdb=" N   VAL A 233 " --> pdb=" O   LYS A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 262
      removed outlier: 3.929A  pdb=" N   GLY A 262 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 314
      removed outlier: 4.648A  pdb=" N   ILE A 293 " --> pdb=" O   SER A 289 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ILE A 294 " --> pdb=" O   ASN A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 324
    Processing helix  chain 'A' and resid 341 through 346
      removed outlier: 3.635A  pdb=" N   TYR A 345 " --> pdb=" O   GLY A 341 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ILE A 346 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 341 through 346'
    Processing helix  chain 'A' and resid 351 through 358
      removed outlier: 3.573A  pdb=" N   ASP A 358 " --> pdb=" O   GLU A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 384
      removed outlier: 3.568A  pdb=" N   CYS A 373 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 399
    Processing helix  chain 'A' and resid 409 through 415
    Processing helix  chain 'A' and resid 417 through 440
    Processing helix  chain 'A' and resid 444 through 466
      removed outlier: 3.521A  pdb=" N   TYR A 458 " --> pdb=" O   THR A 454 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 39
    Processing helix  chain 'C' and resid 43 through 80
      removed outlier: 3.948A  pdb=" N   LYS C  49 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ILE C  73 " --> pdb=" O   LYS C  69 " (cutoff:3.500A)
      Proline residue:  C  74  - end of helix
    Processing helix  chain 'B' and resid 53 through 82
      removed outlier: 3.833A  pdb=" N   GLY B  79 " --> pdb=" O   SER B  75 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LYS B  80 " --> pdb=" O   LYS B  76 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 13 through 36
      removed outlier: 3.751A  pdb=" N   VAL D  25 " --> pdb=" O   GLY D  21 " (cutoff:3.500A)
      Proline residue:  D  28  - end of helix
    Processing helix  chain 'D' and resid 58 through 67
      removed outlier: 4.263A  pdb=" N   LEU D  62 " --> pdb=" O   VAL D  58 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   GLU D  64 " --> pdb=" O   LYS D  60 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   GLU D  65 " --> pdb=" O   ASN D  61 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   TYR D  66 " --> pdb=" O   LEU D  62 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 68 through 78
      removed outlier: 3.513A  pdb=" N   PHE D  74 " --> pdb=" O   GLU D  70 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 94 through 113
    Processing helix  chain 'D' and resid 212 through 217
    Processing helix  chain 'D' and resid 219 through 233
      removed outlier: 3.666A  pdb=" N   LEU D 223 " --> pdb=" O   ALA D 219 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   VAL D 224 " --> pdb=" O   SER D 220 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 233 through 248
    Processing helix  chain 'D' and resid 255 through 268
    Processing helix  chain 'D' and resid 276 through 285
    Processing helix  chain 'D' and resid 287 through 294
      removed outlier: 3.961A  pdb=" N   LYS D 291 " --> pdb=" O   ALA D 287 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLN D 292 " --> pdb=" O   HIS D 288 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 298 through 311
    Processing helix  chain 'D' and resid 318 through 343
      removed outlier: 3.585A  pdb=" N   ARG D 324 " --> pdb=" O   ASN D 320 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   HIS D 330 " --> pdb=" O   VAL D 326 " (cutoff:3.500A)
      removed outlier: 5.400A  pdb=" N   SER D 331 " --> pdb=" O   ALA D 327 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LEU D 332 " --> pdb=" O   LYS D 328 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 345 through 362
      removed outlier: 3.817A  pdb=" N   ALA D 349 " --> pdb=" O   ASN D 345 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 378 through 386
      removed outlier: 4.082A  pdb=" N   THR D 384 " --> pdb=" O   GLU D 380 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 391 through 397
    Processing helix  chain 'D' and resid 399 through 408
      removed outlier: 3.719A  pdb=" N   GLY D 404 " --> pdb=" O   ASP D 400 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 411 through 423
      removed outlier: 4.419A  pdb=" N   GLU D 417 " --> pdb=" O   ALA D 413 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 466 through 470
    Processing helix  chain 'D' and resid 480 through 485
    Processing helix  chain 'D' and resid 490 through 494
      removed outlier: 3.532A  pdb=" N   LYS D 493 " --> pdb=" O   MET D 490 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 537 through 541
    Processing helix  chain 'D' and resid 554 through 558
      removed outlier: 3.518A  pdb=" N   HIS D 558 " --> pdb=" O   LEU D 555 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 71 through 86
      removed outlier: 3.550A  pdb=" N   PHE E  76 " --> pdb=" O   HIS E  72 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLU E  83 " --> pdb=" O   LYS E  79 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ASN E  84 " --> pdb=" O   GLU E  80 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 88 through 124
      removed outlier: 4.137A  pdb=" N   LEU E  92 " --> pdb=" O   HIS E  88 " (cutoff:3.500A)
      Proline residue:  E 115  - end of helix
    Processing helix  chain 'E' and resid 128 through 156
      removed outlier: 3.911A  pdb=" N   LYS E 132 " --> pdb=" O   GLU E 128 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LYS E 139 " --> pdb=" O   GLU E 135 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 160 through 182
      removed outlier: 4.125A  pdb=" N   MET E 165 " --> pdb=" O   GLN E 161 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   PHE E 172 " --> pdb=" O   LYS E 168 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 182 through 195
      removed outlier: 4.429A  pdb=" N   GLU E 188 " --> pdb=" O   LEU E 184 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   CYS E 190 " --> pdb=" O   ARG E 186 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ILE E 191 " --> pdb=" O   LYS E 187 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 199 through 203
      removed outlier: 3.579A  pdb=" N   GLY E 202 " --> pdb=" O   ASN E 199 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ARG E 203 " --> pdb=" O   ASN E 200 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 199 through 203'
    Processing helix  chain 'F' and resid 21 through 41
      removed outlier: 3.731A  pdb=" N   GLY F  40 " --> pdb=" O   THR F  36 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 52 through 71
      removed outlier: 3.865A  pdb=" N   ASN F  68 " --> pdb=" O   SER F  64 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   LEU F  69 " --> pdb=" O   GLY F  65 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   GLN F  70 " --> pdb=" O   MET F  66 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 74 through 91
      removed outlier: 4.011A  pdb=" N   LEU F  78 " --> pdb=" O   LEU F  74 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LYS F  79 " --> pdb=" O   ASN F  75 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 97 through 120
      Proline residue:  F 103  - end of helix
      removed outlier: 3.713A  pdb=" N   SER F 111 " --> pdb=" O   PHE F 107 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 122 through 135
    Processing helix  chain 'F' and resid 139 through 153
      removed outlier: 3.623A  pdb=" N   PHE F 143 " --> pdb=" O   GLN F 139 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   VAL F 144 " --> pdb=" O   PRO F 140 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   ARG F 145 " --> pdb=" O   ASP F 141 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 155 through 168
    Processing helix  chain 'F' and resid 175 through 192
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 211
    Processing sheet with id=AA2, first strand: chain 'A' and resid 279 through 284
      removed outlier: 3.528A  pdb=" N   ILE A 269 " --> pdb=" O   GLY A 279 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   TYR A 281 " --> pdb=" O   LEU A 267 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   LEU A 267 " --> pdb=" O   TYR A 281 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 327
    Processing sheet with id=AA4, first strand: chain 'D' and resid 430 through 436
      removed outlier: 6.726A  pdb=" N   LYS D 454 " --> pdb=" O   ILE D 431 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   ALA D 433 " --> pdb=" O   SER D 452 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   SER D 452 " --> pdb=" O   ALA D 433 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   PHE D 435 " --> pdb=" O   TYR D 450 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   TYR D 450 " --> pdb=" O   PHE D 435 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532
    Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 6

    659 hydrogen bonds defined for protein.
    1926 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: 1.41

  Time building geometry restraints manager: 1.20 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3300
        1.34 -     1.46: 2159
        1.46 -     1.58: 5193
        1.58 -     1.69: 0
        1.69 -     1.81: 61
  Bond restraints: 10713
  Sorted by residual:
  bond pdb=" CB  VAL C  54 "
       pdb=" CG1 VAL C  54 "
    ideal  model  delta    sigma   weight residual
    1.521  1.495  0.026 3.30e-02 9.18e+02 6.34e-01
  bond pdb=" CG1 ILE D 280 "
       pdb=" CD1 ILE D 280 "
    ideal  model  delta    sigma   weight residual
    1.513  1.483  0.030 3.90e-02 6.57e+02 6.07e-01
  bond pdb=" CB  TRP D 283 "
       pdb=" CG  TRP D 283 "
    ideal  model  delta    sigma   weight residual
    1.498  1.475  0.023 3.10e-02 1.04e+03 5.54e-01
  bond pdb=" CB  LEU A 258 "
       pdb=" CG  LEU A 258 "
    ideal  model  delta    sigma   weight residual
    1.530  1.515  0.015 2.00e-02 2.50e+03 5.45e-01
  bond pdb=" CA  LEU A 147 "
       pdb=" C   LEU A 147 "
    ideal  model  delta    sigma   weight residual
    1.525  1.540 -0.015 2.10e-02 2.27e+03 4.89e-01
  ... (remaining 10708 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 14391
        2.03 -     4.05: 114
        4.05 -     6.08: 16
        6.08 -     8.10: 3
        8.10 -    10.13: 2
  Bond angle restraints: 14526
  Sorted by residual:
  angle pdb=" N   VAL D  25 "
        pdb=" CA  VAL D  25 "
        pdb=" C   VAL D  25 "
      ideal   model   delta    sigma   weight residual
     112.96  110.12    2.84 1.00e+00 1.00e+00 8.09e+00
  angle pdb=" CA  LEU A 162 "
        pdb=" CB  LEU A 162 "
        pdb=" CG  LEU A 162 "
      ideal   model   delta    sigma   weight residual
     116.30  125.19   -8.89 3.50e+00 8.16e-02 6.46e+00
  angle pdb=" C   THR A 288 "
        pdb=" N   SER A 289 "
        pdb=" CA  SER A 289 "
      ideal   model   delta    sigma   weight residual
     120.82  124.48   -3.66 1.50e+00 4.44e-01 5.94e+00
  angle pdb=" C   ILE A 418 "
        pdb=" CA  ILE A 418 "
        pdb=" CB  ILE A 418 "
      ideal   model   delta    sigma   weight residual
     114.00  110.89    3.11 1.31e+00 5.83e-01 5.63e+00
  angle pdb=" CA  ILE E 126 "
        pdb=" C   ILE E 126 "
        pdb=" N   GLY E 127 "
      ideal   model   delta    sigma   weight residual
     116.60  120.02   -3.42 1.45e+00 4.76e-01 5.55e+00
  ... (remaining 14521 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.35: 5970
       17.35 -    34.70: 404
       34.70 -    52.06: 60
       52.06 -    69.41: 9
       69.41 -    86.76: 4
  Dihedral angle restraints: 6447
    sinusoidal: 2528
      harmonic: 3919
  Sorted by residual:
  dihedral pdb=" CB  GLU D 472 "
           pdb=" CG  GLU D 472 "
           pdb=" CD  GLU D 472 "
           pdb=" OE1 GLU D 472 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.76  -86.76     1      3.00e+01 1.11e-03 1.01e+01
  dihedral pdb=" N   LYS A  26 "
           pdb=" CA  LYS A  26 "
           pdb=" CB  LYS A  26 "
           pdb=" CG  LYS A  26 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.51  -59.49     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CB  MET A 158 "
           pdb=" CG  MET A 158 "
           pdb=" SD  MET A 158 "
           pdb=" CE  MET A 158 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  114.89  -54.89     3      1.50e+01 4.44e-03 9.31e+00
  ... (remaining 6444 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1052
       0.028 -    0.056: 440
       0.056 -    0.084: 150
       0.084 -    0.113: 72
       0.113 -    0.141: 10
  Chirality restraints: 1724
  Sorted by residual:
  chirality pdb=" CA  THR A 291 "
            pdb=" N   THR A 291 "
            pdb=" C   THR A 291 "
            pdb=" CB  THR A 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.39    0.14 2.00e-01 2.50e+01 4.95e-01
  chirality pdb=" CA  ILE D 470 "
            pdb=" N   ILE D 470 "
            pdb=" C   ILE D 470 "
            pdb=" CB  ILE D 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.16e-01
  chirality pdb=" CA  ILE D 573 "
            pdb=" N   ILE D 573 "
            pdb=" C   ILE D 573 "
            pdb=" CB  ILE D 573 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.95e-01
  ... (remaining 1721 not shown)

  Planarity restraints: 1806
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA F  93 "   -0.023 5.00e-02 4.00e+02   3.48e-02 1.93e+00
        pdb=" N   PRO F  94 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO F  94 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO F  94 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR F  47 "    0.022 5.00e-02 4.00e+02   3.37e-02 1.82e+00
        pdb=" N   PRO F  48 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO F  48 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO F  48 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D 462 "   -0.019 5.00e-02 4.00e+02   2.84e-02 1.29e+00
        pdb=" N   PRO D 463 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO D 463 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO D 463 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 1803 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1107
        2.74 -     3.28: 10975
        3.28 -     3.82: 17200
        3.82 -     4.36: 18852
        4.36 -     4.90: 33379
  Nonbonded interactions: 81513
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG F  92 "
            pdb=" OE1 GLU F  96 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" OG  SER A 179 "
            pdb=" OG  SER A 182 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   LYS E  79 "
            pdb=" OG  SER E  82 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O   THR D 444 "
            pdb=" OG  SER D 447 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OG1 THR A 441 "
            pdb=" O   GLY A 443 "
     model   vdw
     2.250 3.040
  ... (remaining 81508 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:             1.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     9.630
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
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      :  0.003   0.030  10713  Z= 0.140
  Angle     :  0.531  10.125  14526  Z= 0.297
  Chirality :  0.038   0.141   1724
  Planarity :  0.003   0.035   1806
  Dihedral  : 11.866  86.758   3903
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.25 (0.22), residues: 1325
  helix:  0.01 (0.17), residues: 817
  sheet: -2.62 (0.48), residues: 80
  loop : -1.95 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 238 
 TYR   0.009   0.001   TYR F 190 
 PHE   0.014   0.001   PHE A 304 
 TRP   0.008   0.001   TRP D 513 
 HIS   0.004   0.001   HIS D 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (10713)
  covalent geometry    : angle       0.53145 (14526)
  hydrogen bonds       : bond        0.14078 (  659)
  hydrogen bonds       : angle       5.19628 ( 1926)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   66 TYR cc_start: 0.8708 (t80) cc_final: 0.8330 (t80)
REVERT: B   59 PHE cc_start: 0.8215 (m-10) cc_final: 0.7815 (t80)
REVERT: D   14 TRP cc_start: 0.8789 (p-90) cc_final: 0.8333 (p-90)
REVERT: D   19 LEU cc_start: 0.9416 (mt) cc_final: 0.9157 (mt)
REVERT: D  491 MET cc_start: 0.9312 (ttp) cc_final: 0.9061 (tmm)
REVERT: D  608 MET cc_start: 0.8568 (ptp) cc_final: 0.8256 (ttp)
REVERT: E   75 TYR cc_start: 0.8500 (t80) cc_final: 0.8217 (t80)
REVERT: F  114 ASP cc_start: 0.9326 (t0) cc_final: 0.8947 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1036
  time to fit residues: 14.6661
Evaluate side-chains
  57 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    0.0070
   overall best weight:    2.9604

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN
A 192 GLN
A 403 ASN
D 282 HIS
D 292 GLN
D 307 GLN
D 494 GLN
D 558 HIS
E  98 ASN
E 173 ASN
** F  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.047653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.036043 restraints weight = 75078.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.037109 restraints weight = 39501.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.037824 restraints weight = 25902.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.038274 restraints weight = 19539.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.038625 restraints weight = 16261.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10713  Z= 0.173
  Angle     :  0.584  11.624  14526  Z= 0.289
  Chirality :  0.040   0.195   1724
  Planarity :  0.004   0.036   1806
  Dihedral  :  3.448  16.320   1429
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  9.54 %
    Favored  : 89.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.23), residues: 1325
  helix:  1.12 (0.18), residues: 833
  sheet: -1.53 (0.58), residues: 65
  loop : -1.62 (0.28), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F 110 
 TYR   0.011   0.001   TYR F 190 
 PHE   0.019   0.001   PHE A 304 
 TRP   0.009   0.001   TRP A  35 
 HIS   0.004   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (10713)
  covalent geometry    : angle       0.58432 (14526)
  hydrogen bonds       : bond        0.03564 (  659)
  hydrogen bonds       : angle       4.03115 ( 1926)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   56 ILE cc_start: 0.7497 (pt) cc_final: 0.7060 (tp)
REVERT: C   66 TYR cc_start: 0.8677 (t80) cc_final: 0.8332 (t80)
REVERT: B   59 PHE cc_start: 0.8153 (m-10) cc_final: 0.7842 (t80)
REVERT: D   14 TRP cc_start: 0.8962 (p-90) cc_final: 0.8441 (p-90)
REVERT: D   19 LEU cc_start: 0.9398 (mt) cc_final: 0.9159 (mt)
REVERT: E   87 ILE cc_start: 0.8257 (pt) cc_final: 0.8039 (pt)
REVERT: F  114 ASP cc_start: 0.9458 (t0) cc_final: 0.9236 (t0)
  outliers start: 10
  outliers final: 4
  residues processed: 76
  average time/residue: 0.0814
  time to fit residues: 9.4754
Evaluate side-chains
  68 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain E residue  201 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 101 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 98 optimal weight:    8.9990
   chunk 108 optimal weight:    6.9990
   chunk 79 optimal weight:    7.9990
   chunk 45 optimal weight:   20.0000
   chunk 105 optimal weight:    7.9990
   chunk 68 optimal weight:    4.9990
   chunk 30 optimal weight:   30.0000
   chunk 106 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** D 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 311 ASN
E  72 HIS
** F  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.046279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.034663 restraints weight = 76876.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.035701 restraints weight = 40944.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.036380 restraints weight = 27069.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.036876 restraints weight = 20533.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.037101 restraints weight = 16984.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.1804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  10713  Z= 0.235
  Angle     :  0.632  13.155  14526  Z= 0.311
  Chirality :  0.041   0.151   1724
  Planarity :  0.004   0.038   1806
  Dihedral  :  3.696  17.454   1429
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 13.46 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.23), residues: 1325
  helix:  1.49 (0.18), residues: 829
  sheet: -0.97 (0.59), residues: 75
  loop : -1.27 (0.29), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F 177 
 TYR   0.013   0.001   TYR F 190 
 PHE   0.014   0.001   PHE D 481 
 TRP   0.012   0.001   TRP D 513 
 HIS   0.006   0.002   HIS D 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00510 (10713)
  covalent geometry    : angle       0.63246 (14526)
  hydrogen bonds       : bond        0.03546 (  659)
  hydrogen bonds       : angle       4.09640 ( 1926)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   56 ILE cc_start: 0.7541 (pt) cc_final: 0.7104 (tp)
REVERT: C   66 TYR cc_start: 0.8808 (t80) cc_final: 0.8242 (t80)
REVERT: B   59 PHE cc_start: 0.8417 (m-10) cc_final: 0.8045 (t80)
REVERT: D   14 TRP cc_start: 0.9102 (p-90) cc_final: 0.8523 (p-90)
REVERT: D   19 LEU cc_start: 0.9425 (mt) cc_final: 0.9159 (mt)
REVERT: E   87 ILE cc_start: 0.8281 (pt) cc_final: 0.7943 (pt)
REVERT: F   90 ARG cc_start: 0.9316 (tpp80) cc_final: 0.8958 (mmp80)
REVERT: F  114 ASP cc_start: 0.9523 (t0) cc_final: 0.9311 (t0)
  outliers start: 14
  outliers final: 9
  residues processed: 74
  average time/residue: 0.0683
  time to fit residues: 8.1302
Evaluate side-chains
  69 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  343 PHE
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  170 ILE
Chi-restraints excluded: chain E residue  201 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 58 optimal weight:    9.9990
   chunk 72 optimal weight:    1.9990
   chunk 81 optimal weight:    6.9990
   chunk 113 optimal weight:    4.9990
   chunk 69 optimal weight:    5.9990
   chunk 114 optimal weight:    9.9990
   chunk 31 optimal weight:   20.0000
   chunk 106 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
D 288 HIS
** F  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.046756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.035197 restraints weight = 76507.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.036264 restraints weight = 40278.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.036988 restraints weight = 26422.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.037441 restraints weight = 19945.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.037689 restraints weight = 16619.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10713  Z= 0.160
  Angle     :  0.575  11.855  14526  Z= 0.279
  Chirality :  0.040   0.139   1724
  Planarity :  0.003   0.036   1806
  Dihedral  :  3.590  17.255   1429
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 15.42 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.24), residues: 1325
  helix:  1.73 (0.18), residues: 828
  sheet: -0.82 (0.63), residues: 65
  loop : -1.03 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 110 
 TYR   0.012   0.001   TYR F 190 
 PHE   0.010   0.001   PHE A 304 
 TRP   0.009   0.001   TRP A  35 
 HIS   0.004   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (10713)
  covalent geometry    : angle       0.57547 (14526)
  hydrogen bonds       : bond        0.03320 (  659)
  hydrogen bonds       : angle       3.93113 ( 1926)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   56 ILE cc_start: 0.7556 (pt) cc_final: 0.7126 (tp)
REVERT: C   66 TYR cc_start: 0.8790 (t80) cc_final: 0.8086 (t80)
REVERT: B   59 PHE cc_start: 0.8481 (m-10) cc_final: 0.8053 (t80)
REVERT: D   19 LEU cc_start: 0.9428 (mt) cc_final: 0.9177 (mt)
REVERT: D  265 ASN cc_start: 0.8669 (m-40) cc_final: 0.8419 (m-40)
REVERT: E   87 ILE cc_start: 0.8296 (pt) cc_final: 0.7956 (pt)
REVERT: F   87 MET cc_start: 0.8947 (mpp) cc_final: 0.8700 (mpp)
REVERT: F   90 ARG cc_start: 0.9360 (tpp80) cc_final: 0.8946 (mmp80)
REVERT: F  114 ASP cc_start: 0.9519 (t0) cc_final: 0.9297 (t0)
  outliers start: 16
  outliers final: 9
  residues processed: 79
  average time/residue: 0.0744
  time to fit residues: 9.3647
Evaluate side-chains
  74 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain D residue  274 ILE
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  343 PHE
Chi-restraints excluded: chain D residue  360 VAL
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  201 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 123 optimal weight:    1.9990
   chunk 112 optimal weight:    5.9990
   chunk 105 optimal weight:    9.9990
   chunk 3 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 83 optimal weight:    0.3980
   chunk 129 optimal weight:    0.9980
   chunk 61 optimal weight:    9.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 302 ASN
** F  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 106 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.047524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.035994 restraints weight = 75904.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.037088 restraints weight = 39877.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.037850 restraints weight = 26123.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.038297 restraints weight = 19609.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.038585 restraints weight = 16256.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10713  Z= 0.105
  Angle     :  0.543  10.490  14526  Z= 0.258
  Chirality :  0.039   0.221   1724
  Planarity :  0.003   0.032   1806
  Dihedral  :  3.392  16.646   1429
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 16.04 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (0.24), residues: 1325
  helix:  1.97 (0.18), residues: 832
  sheet: -0.66 (0.64), residues: 65
  loop : -0.73 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 110 
 TYR   0.010   0.001   TYR F 190 
 PHE   0.010   0.001   PHE A 304 
 TRP   0.013   0.001   TRP D  14 
 HIS   0.003   0.001   HIS D 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (10713)
  covalent geometry    : angle       0.54327 (14526)
  hydrogen bonds       : bond        0.03082 (  659)
  hydrogen bonds       : angle       3.71273 ( 1926)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 MET cc_start: 0.9221 (tpp) cc_final: 0.8952 (tpp)
REVERT: C   56 ILE cc_start: 0.7460 (pt) cc_final: 0.7064 (tp)
REVERT: C   66 TYR cc_start: 0.8766 (t80) cc_final: 0.8034 (t80)
REVERT: B   59 PHE cc_start: 0.8461 (m-10) cc_final: 0.8031 (t80)
REVERT: D   19 LEU cc_start: 0.9439 (mt) cc_final: 0.9168 (mt)
REVERT: E   76 PHE cc_start: 0.8923 (m-80) cc_final: 0.8662 (m-80)
REVERT: E   87 ILE cc_start: 0.8286 (pt) cc_final: 0.7917 (pt)
REVERT: F   87 MET cc_start: 0.8899 (mpp) cc_final: 0.8372 (mpp)
REVERT: F   90 ARG cc_start: 0.9376 (tpp80) cc_final: 0.9161 (mtm110)
REVERT: F  114 ASP cc_start: 0.9445 (t0) cc_final: 0.9223 (t0)
  outliers start: 15
  outliers final: 5
  residues processed: 84
  average time/residue: 0.0760
  time to fit residues: 9.9850
Evaluate side-chains
  70 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  343 PHE
Chi-restraints excluded: chain D residue  516 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 125 optimal weight:   10.0000
   chunk 23 optimal weight:    6.9990
   chunk 21 optimal weight:    0.6980
   chunk 70 optimal weight:    8.9990
   chunk 88 optimal weight:    9.9990
   chunk 41 optimal weight:    7.9990
   chunk 74 optimal weight:    0.9990
   chunk 86 optimal weight:    0.4980
   chunk 111 optimal weight:    5.9990
   chunk 31 optimal weight:    8.9990
   chunk 106 optimal weight:    7.9990
   overall best weight:    3.0386

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

Flipped N/Q/H residues before XYZ refinement:
** E  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.046746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.035212 restraints weight = 77455.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.036280 restraints weight = 40863.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.036992 restraints weight = 26830.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.037489 restraints weight = 20261.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.037772 restraints weight = 16793.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.2820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.2256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10713  Z= 0.171
  Angle     :  0.593  12.790  14526  Z= 0.284
  Chirality :  0.041   0.334   1724
  Planarity :  0.003   0.033   1806
  Dihedral  :  3.458  16.955   1429
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 16.31 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.57 (0.24), residues: 1325
  helix:  1.99 (0.18), residues: 831
  sheet: -0.66 (0.65), residues: 65
  loop : -0.56 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 186 
 TYR   0.013   0.001   TYR F 190 
 PHE   0.025   0.001   PHE A 304 
 TRP   0.026   0.001   TRP D  14 
 HIS   0.004   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (10713)
  covalent geometry    : angle       0.59263 (14526)
  hydrogen bonds       : bond        0.03156 (  659)
  hydrogen bonds       : angle       3.83305 ( 1926)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 MET cc_start: 0.9287 (tpp) cc_final: 0.9078 (mmm)
REVERT: A  400 MET cc_start: 0.8911 (tpp) cc_final: 0.8686 (tpp)
REVERT: C   56 ILE cc_start: 0.7500 (pt) cc_final: 0.7099 (tp)
REVERT: C   66 TYR cc_start: 0.8707 (t80) cc_final: 0.8076 (t80)
REVERT: B   59 PHE cc_start: 0.8486 (m-10) cc_final: 0.8052 (t80)
REVERT: D   14 TRP cc_start: 0.8876 (p-90) cc_final: 0.8323 (p-90)
REVERT: D   19 LEU cc_start: 0.9449 (mt) cc_final: 0.9160 (mt)
REVERT: E   87 ILE cc_start: 0.8348 (pt) cc_final: 0.7975 (pt)
REVERT: F   90 ARG cc_start: 0.9371 (tpp80) cc_final: 0.9168 (mtm110)
  outliers start: 21
  outliers final: 13
  residues processed: 81
  average time/residue: 0.0711
  time to fit residues: 9.3455
Evaluate side-chains
  76 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain D residue  274 ILE
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  343 PHE
Chi-restraints excluded: chain D residue  355 THR
Chi-restraints excluded: chain D residue  360 VAL
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  201 ASP
Chi-restraints excluded: chain F residue  109 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 108 optimal weight:    6.9990
   chunk 113 optimal weight:    2.9990
   chunk 31 optimal weight:   30.0000
   chunk 129 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 131 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 79 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   chunk 123 optimal weight:    0.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** E  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.046821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2736 r_free = 0.2736 target = 0.035306 restraints weight = 76344.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.036379 restraints weight = 40532.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.037098 restraints weight = 26698.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.037543 restraints weight = 20242.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.037871 restraints weight = 16833.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10713  Z= 0.149
  Angle     :  0.589  11.936  14526  Z= 0.278
  Chirality :  0.040   0.284   1724
  Planarity :  0.003   0.031   1806
  Dihedral  :  3.464  16.974   1429
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 16.76 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.24), residues: 1325
  helix:  2.02 (0.18), residues: 834
  sheet: -0.56 (0.66), residues: 65
  loop : -0.42 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 186 
 TYR   0.013   0.001   TYR F 190 
 PHE   0.025   0.001   PHE A 304 
 TRP   0.020   0.001   TRP D  14 
 HIS   0.004   0.001   HIS E  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (10713)
  covalent geometry    : angle       0.58911 (14526)
  hydrogen bonds       : bond        0.03108 (  659)
  hydrogen bonds       : angle       3.76446 ( 1926)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 63
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 MET cc_start: 0.9284 (tpp) cc_final: 0.9050 (mmm)
REVERT: A  400 MET cc_start: 0.8956 (tpp) cc_final: 0.8743 (tpp)
REVERT: C   56 ILE cc_start: 0.7492 (pt) cc_final: 0.7100 (tp)
REVERT: C   66 TYR cc_start: 0.8701 (t80) cc_final: 0.8038 (t80)
REVERT: B   59 PHE cc_start: 0.8526 (m-10) cc_final: 0.8074 (t80)
REVERT: D   14 TRP cc_start: 0.8997 (p-90) cc_final: 0.8395 (p-90)
REVERT: D   19 LEU cc_start: 0.9434 (mt) cc_final: 0.9130 (mt)
REVERT: E   87 ILE cc_start: 0.8198 (pt) cc_final: 0.7984 (pt)
REVERT: F   90 ARG cc_start: 0.9369 (tpp80) cc_final: 0.9164 (mtm110)
  outliers start: 22
  outliers final: 14
  residues processed: 81
  average time/residue: 0.0772
  time to fit residues: 10.1141
Evaluate side-chains
  75 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain D residue  274 ILE
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  343 PHE
Chi-restraints excluded: chain D residue  360 VAL
Chi-restraints excluded: chain D residue  516 LEU
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  201 ASP
Chi-restraints excluded: chain F residue  109 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 91 optimal weight:    6.9990
   chunk 59 optimal weight:   10.0000
   chunk 19 optimal weight:    7.9990
   chunk 34 optimal weight:   10.0000
   chunk 114 optimal weight:    5.9990
   chunk 116 optimal weight:    8.9990
   chunk 123 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 38 optimal weight:    0.5980
   chunk 53 optimal weight:    6.9990
   chunk 78 optimal weight:   10.0000
   overall best weight:    3.7186

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

Flipped N/Q/H residues before XYZ refinement:
** E  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.046118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.034816 restraints weight = 75862.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2753 r_free = 0.2753 target = 0.035825 restraints weight = 39801.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.036509 restraints weight = 26187.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.036968 restraints weight = 19786.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.037175 restraints weight = 16491.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.2611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10713  Z= 0.202
  Angle     :  0.646  12.047  14526  Z= 0.307
  Chirality :  0.041   0.278   1724
  Planarity :  0.004   0.033   1806
  Dihedral  :  3.637  17.602   1429
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 17.83 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.24), residues: 1325
  helix:  1.88 (0.18), residues: 841
  sheet: -0.57 (0.62), residues: 75
  loop : -0.52 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 186 
 TYR   0.015   0.001   TYR F 190 
 PHE   0.025   0.001   PHE A 304 
 TRP   0.016   0.001   TRP D  14 
 HIS   0.005   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 (10713)
  covalent geometry    : angle       0.64588 (14526)
  hydrogen bonds       : bond        0.03320 (  659)
  hydrogen bonds       : angle       3.94355 ( 1926)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 60
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 MET cc_start: 0.9303 (tpp) cc_final: 0.9055 (mmm)
REVERT: C   56 ILE cc_start: 0.7532 (pt) cc_final: 0.7128 (tp)
REVERT: C   66 TYR cc_start: 0.8773 (t80) cc_final: 0.8034 (t80)
REVERT: B   59 PHE cc_start: 0.8578 (m-10) cc_final: 0.8189 (t80)
REVERT: D  490 MET cc_start: 0.9053 (tmm) cc_final: 0.8843 (tmm)
REVERT: F   90 ARG cc_start: 0.9380 (tpp80) cc_final: 0.9132 (mtm110)
REVERT: F  114 ASP cc_start: 0.9446 (t0) cc_final: 0.8950 (p0)
  outliers start: 22
  outliers final: 16
  residues processed: 77
  average time/residue: 0.0699
  time to fit residues: 8.9120
Evaluate side-chains
  75 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 59
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain D residue  274 ILE
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  343 PHE
Chi-restraints excluded: chain D residue  355 THR
Chi-restraints excluded: chain D residue  360 VAL
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  201 ASP
Chi-restraints excluded: chain F residue  109 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 41 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9990
   chunk 110 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 92 optimal weight:    6.9990
   chunk 72 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** E  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.046779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2740 r_free = 0.2740 target = 0.035446 restraints weight = 75603.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.036494 restraints weight = 39545.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.037200 restraints weight = 25826.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.037682 restraints weight = 19402.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.038035 restraints weight = 16046.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.2653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10713  Z= 0.132
  Angle     :  0.606  11.276  14526  Z= 0.283
  Chirality :  0.041   0.272   1724
  Planarity :  0.003   0.034   1806
  Dihedral  :  3.541  17.007   1429
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 18.36 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.24), residues: 1325
  helix:  2.00 (0.18), residues: 838
  sheet: -0.51 (0.66), residues: 65
  loop : -0.37 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 186 
 TYR   0.012   0.001   TYR F 190 
 PHE   0.025   0.001   PHE A 304 
 TRP   0.035   0.001   TRP D  14 
 HIS   0.003   0.001   HIS E  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (10713)
  covalent geometry    : angle       0.60615 (14526)
  hydrogen bonds       : bond        0.03132 (  659)
  hydrogen bonds       : angle       3.78975 ( 1926)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 MET cc_start: 0.9278 (tpp) cc_final: 0.9049 (mmm)
REVERT: C   56 ILE cc_start: 0.7469 (pt) cc_final: 0.7082 (tp)
REVERT: C   66 TYR cc_start: 0.8735 (t80) cc_final: 0.8017 (t80)
REVERT: B   59 PHE cc_start: 0.8451 (m-10) cc_final: 0.8113 (t80)
REVERT: D   14 TRP cc_start: 0.8917 (p-90) cc_final: 0.8424 (p-90)
REVERT: D   19 LEU cc_start: 0.9411 (mt) cc_final: 0.9158 (mm)
REVERT: D  490 MET cc_start: 0.9020 (tmm) cc_final: 0.8805 (tmm)
REVERT: F   90 ARG cc_start: 0.9361 (tpp80) cc_final: 0.8980 (mmp80)
  outliers start: 19
  outliers final: 17
  residues processed: 77
  average time/residue: 0.0733
  time to fit residues: 9.2277
Evaluate side-chains
  75 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 VAL
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain D residue  274 ILE
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  343 PHE
Chi-restraints excluded: chain D residue  360 VAL
Chi-restraints excluded: chain D residue  516 LEU
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  198 ILE
Chi-restraints excluded: chain E residue  201 ASP
Chi-restraints excluded: chain F residue  109 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   chunk 95 optimal weight:    7.9990
   chunk 78 optimal weight:   10.0000
   chunk 76 optimal weight:    3.9990
   chunk 60 optimal weight:    0.5980
   chunk 88 optimal weight:    1.9990
   chunk 73 optimal weight:    8.9990
   chunk 14 optimal weight:    0.7980
   chunk 62 optimal weight:    5.9990
   chunk 71 optimal weight:    0.3980
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** E  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.047112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.035711 restraints weight = 74910.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.036778 restraints weight = 39452.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.037482 restraints weight = 25892.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.037978 restraints weight = 19523.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.038320 restraints weight = 16153.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.2734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10713  Z= 0.118
  Angle     :  0.606  11.452  14526  Z= 0.282
  Chirality :  0.040   0.256   1724
  Planarity :  0.003   0.033   1806
  Dihedral  :  3.465  16.723   1429
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 19.25 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.78 (0.24), residues: 1325
  helix:  2.06 (0.18), residues: 840
  sheet: -0.73 (0.59), residues: 77
  loop : -0.24 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 186 
 TYR   0.011   0.001   TYR F 190 
 PHE   0.025   0.001   PHE A 304 
 TRP   0.032   0.001   TRP D  14 
 HIS   0.003   0.001   HIS E  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (10713)
  covalent geometry    : angle       0.60646 (14526)
  hydrogen bonds       : bond        0.03082 (  659)
  hydrogen bonds       : angle       3.68870 ( 1926)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.7515 (ttt) cc_final: 0.6479 (ptm)
REVERT: A  249 MET cc_start: 0.9257 (tpp) cc_final: 0.9048 (mmm)
REVERT: C   56 ILE cc_start: 0.7670 (pt) cc_final: 0.7267 (tp)
REVERT: C   66 TYR cc_start: 0.8700 (t80) cc_final: 0.8055 (t80)
REVERT: B   59 PHE cc_start: 0.8440 (m-10) cc_final: 0.8085 (t80)
REVERT: D   14 TRP cc_start: 0.8937 (p-90) cc_final: 0.8442 (p-90)
REVERT: D   19 LEU cc_start: 0.9404 (mt) cc_final: 0.9145 (mm)
REVERT: F   90 ARG cc_start: 0.9357 (tpp80) cc_final: 0.9152 (mtm110)
  outliers start: 16
  outliers final: 14
  residues processed: 71
  average time/residue: 0.0834
  time to fit residues: 9.5720
Evaluate side-chains
  73 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain D residue  274 ILE
Chi-restraints excluded: chain D residue  275 VAL
Chi-restraints excluded: chain D residue  343 PHE
Chi-restraints excluded: chain D residue  360 VAL
Chi-restraints excluded: chain D residue  516 LEU
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  191 ILE
Chi-restraints excluded: chain E residue  198 ILE
Chi-restraints excluded: chain E residue  201 ASP
Chi-restraints excluded: chain F residue  109 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0470
   chunk 4 optimal weight:    0.0770
   chunk 88 optimal weight:    0.6980
   chunk 58 optimal weight:   10.0000
   chunk 43 optimal weight:   10.0000
   chunk 26 optimal weight:    6.9990
   chunk 97 optimal weight:    3.9990
   chunk 129 optimal weight:    9.9990
   chunk 44 optimal weight:    9.9990
   overall best weight:    0.9640

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN
E  88 HIS
** F  68 ASN ** 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 = 0.3175 r_free = 0.3175 target = 0.047722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.036353 restraints weight = 75575.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.037436 restraints weight = 39504.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.038159 restraints weight = 25795.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.038683 restraints weight = 19339.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.038942 restraints weight = 15902.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.2833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10713  Z= 0.103
  Angle     :  0.609  15.531  14526  Z= 0.278
  Chirality :  0.041   0.349   1724
  Planarity :  0.003   0.032   1806
  Dihedral  :  3.334  16.363   1429
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 19.79 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.93 (0.24), residues: 1325
  helix:  2.16 (0.18), residues: 840
  sheet: -0.70 (0.58), residues: 79
  loop : -0.14 (0.33), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 186 
 TYR   0.009   0.001   TYR F 190 
 PHE   0.025   0.001   PHE A 304 
 TRP   0.032   0.001   TRP D  14 
 HIS   0.006   0.001   HIS C  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (10713)
  covalent geometry    : angle       0.60931 (14526)
  hydrogen bonds       : bond        0.02917 (  659)
  hydrogen bonds       : angle       3.57820 ( 1926)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1542.59 seconds
wall clock time: 27 minutes 41.04 seconds (1661.04 seconds total)